diff --git a/packages/core/src/libraries/protected-app.test.ts b/packages/core/src/libraries/protected-app.test.ts
index 14cdf0354..05eb9021e 100644
--- a/packages/core/src/libraries/protected-app.test.ts
+++ b/packages/core/src/libraries/protected-app.test.ts
@@ -18,12 +18,13 @@ import { mockFallbackOrigin } from '#src/utils/cloudflare/mock.js';
 const { jest } = import.meta;
 const { mockEsmWithActual } = createMockUtils(jest);
 
-const { updateProtectedAppSiteConfigs } = await mockEsmWithActual(
+const { updateProtectedAppSiteConfigs, deleteCustomHostname } = await mockEsmWithActual(
   '#src/utils/cloudflare/index.js',
   () => ({
     updateProtectedAppSiteConfigs: jest.fn(),
     getCustomHostname: jest.fn(async () => mockCloudflareData),
     getFallbackOrigin: jest.fn(async () => mockFallbackOrigin),
+    deleteCustomHostname: jest.fn(),
   })
 );
 
@@ -36,12 +37,12 @@ const updateApplicationById = jest.fn(async (id: string, data: Partial<Applicati
   ...mockProtectedApplication,
   ...data,
 }));
-
 const {
   syncAppConfigsToRemote,
   checkAndBuildProtectedAppData,
   syncAppCustomDomainStatus,
   getDefaultDomain,
+  deleteDomainFromRemote,
 } = createProtectedAppLibrary(
   new MockQueries({
     applications: {
@@ -222,3 +223,10 @@ describe('syncAppCustomDomainStatus()', () => {
     expect(updateApplicationById).not.toHaveBeenCalled();
   });
 });
+
+describe('deleteDomainFromRemote()', () => {
+  it('should call deleteCustomHostname', async () => {
+    await deleteDomainFromRemote('id');
+    expect(deleteCustomHostname).toHaveBeenCalled();
+  });
+});
diff --git a/packages/core/src/libraries/protected-app.ts b/packages/core/src/libraries/protected-app.ts
index 55e3175f6..fa9b7e37e 100644
--- a/packages/core/src/libraries/protected-app.ts
+++ b/packages/core/src/libraries/protected-app.ts
@@ -17,6 +17,7 @@ import SystemContext from '#src/tenants/SystemContext.js';
 import assertThat from '#src/utils/assert-that.js';
 import {
   createCustomHostname,
+  deleteCustomHostname,
   deleteProtectedAppSiteConfigs,
   getCustomHostname,
   getDomainStatusFromCloudflareData,
@@ -95,6 +96,14 @@ const addDomainToRemote = async (
   };
 };
 
+/**
+ * Call Cloudflare API to delete the domain (custom hostname)
+ */
+const deleteDomainFromRemote = async (id: string) => {
+  const hostnameProviderConfig = await getHostnameProviderConfig();
+  await deleteCustomHostname(hostnameProviderConfig, id);
+};
+
 export const createProtectedAppLibrary = (queries: Queries) => {
   const {
     applications: { findApplicationById, findApplicationByProtectedAppHost, updateApplicationById },
@@ -274,5 +283,6 @@ export const createProtectedAppLibrary = (queries: Queries) => {
     getDefaultDomain,
     addDomainToRemote,
     syncAppCustomDomainStatus,
+    deleteDomainFromRemote,
   };
 };
diff --git a/packages/core/src/routes/applications/application-protected-app-metadata.openapi.json b/packages/core/src/routes/applications/application-protected-app-metadata.openapi.json
index 24f99d1c2..039c90862 100644
--- a/packages/core/src/routes/applications/application-protected-app-metadata.openapi.json
+++ b/packages/core/src/routes/applications/application-protected-app-metadata.openapi.json
@@ -41,6 +41,20 @@
           }
         }
       }
+    },
+    "/api/applications/{id}/protected-app-metadata/custom-domains/{domain}": {
+      "delete": {
+        "summary": "Delete a custom domain.",
+        "description": "Add a custom domain.",
+        "responses": {
+          "204": {
+            "description": "The domain has been deleted."
+          },
+          "404": {
+            "description": "Can not find the domain."
+          }
+        }
+      }
     }
   }
 }
diff --git a/packages/core/src/routes/applications/application-protected-app-metadata.test.ts b/packages/core/src/routes/applications/application-protected-app-metadata.test.ts
index a9415e40b..e41eeae1e 100644
--- a/packages/core/src/routes/applications/application-protected-app-metadata.test.ts
+++ b/packages/core/src/routes/applications/application-protected-app-metadata.test.ts
@@ -2,7 +2,7 @@ import { type Application, DomainStatus } from '@logto/schemas';
 import { pickDefault } from '@logto/shared/esm';
 import { type Nullable } from '@silverhand/essentials';
 
-import { mockProtectedApplication } from '#src/__mocks__/index.js';
+import { mockCloudflareData, mockProtectedApplication } from '#src/__mocks__/index.js';
 import { mockIdGenerators } from '#src/test-utils/nanoid.js';
 import { MockTenant } from '#src/test-utils/tenant.js';
 
@@ -38,6 +38,8 @@ const syncAppCustomDomainStatus = jest.fn(async () => ({
   },
 }));
 const syncAppConfigsToRemote = jest.fn();
+const deleteDomainFromRemote = jest.fn();
+const deleteRemoteAppConfigs = jest.fn();
 
 await mockIdGenerators();
 
@@ -52,7 +54,13 @@ const tenantContext = new MockTenant(
   },
   undefined,
   {
-    protectedApps: { addDomainToRemote, syncAppCustomDomainStatus, syncAppConfigsToRemote },
+    protectedApps: {
+      addDomainToRemote,
+      syncAppCustomDomainStatus,
+      syncAppConfigsToRemote,
+      deleteDomainFromRemote,
+      deleteRemoteAppConfigs,
+    },
     applications: { validateProtectedApplicationById: jest.fn() },
   }
 );
@@ -63,6 +71,10 @@ const applicationProtectedAppMetadataRoutes = await pickDefault(
 );
 
 describe('application protected app metadata routes', () => {
+  afterEach(() => {
+    updateApplicationById.mockClear();
+  });
+
   const requester = createRequester({
     authedRoutes: applicationProtectedAppMetadataRoutes,
     tenantContext,
@@ -131,4 +143,51 @@ describe('application protected app metadata routes', () => {
       expect(response.status).toEqual(422);
     });
   });
+
+  describe('DELETE /applications/:applicationId/protected-app-metadata/custom-domains/:domain', () => {
+    it('should update application, delete remote domain, and delete site configs', async () => {
+      findApplicationById.mockResolvedValueOnce({
+        ...mockProtectedApplication,
+        protectedAppMetadata: {
+          ...mockProtectedApplication.protectedAppMetadata,
+          customDomains: [
+            {
+              ...mockDomainResponse,
+              cloudflareData: mockCloudflareData,
+            },
+          ],
+        },
+      });
+      const response = await requester.delete(
+        `/applications/${mockProtectedApplication.id}/protected-app-metadata/custom-domains/${mockDomainResponse.domain}`
+      );
+      expect(response.status).toEqual(204);
+      expect(updateApplicationById).toHaveBeenCalledWith(mockProtectedApplication.id, {
+        protectedAppMetadata: {
+          ...mockProtectedApplication.protectedAppMetadata,
+          customDomains: [],
+        },
+        oidcClientMetadata: {
+          postLogoutRedirectUris: [`https://${mockProtectedApplication.protectedAppMetadata.host}`],
+          redirectUris: [`https://${mockProtectedApplication.protectedAppMetadata.host}/callback`],
+        },
+      });
+      expect(deleteDomainFromRemote).toHaveBeenCalledWith(mockCloudflareData.id);
+      expect(deleteRemoteAppConfigs).toHaveBeenCalledWith(mockDomainResponse.domain);
+    });
+
+    it('throw when domain exists', async () => {
+      findApplicationById.mockResolvedValueOnce({
+        ...mockProtectedApplication,
+        protectedAppMetadata: {
+          ...mockProtectedApplication.protectedAppMetadata,
+          customDomains: [mockDomainResponse],
+        },
+      });
+      const response = await requester.delete(
+        `/applications/${mockProtectedApplication.id}/protected-app-metadata/custom-domains/unexists.com`
+      );
+      expect(response.status).toEqual(404);
+    });
+  });
 });
diff --git a/packages/core/src/routes/applications/application-protected-app-metadata.ts b/packages/core/src/routes/applications/application-protected-app-metadata.ts
index 867b776e6..104dbb633 100644
--- a/packages/core/src/routes/applications/application-protected-app-metadata.ts
+++ b/packages/core/src/routes/applications/application-protected-app-metadata.ts
@@ -20,7 +20,13 @@ export default function applicationProtectedAppMetadataRoutes<T extends AuthedRo
       },
       libraries: {
         applications: { validateProtectedApplicationById },
-        protectedApps: { addDomainToRemote, syncAppCustomDomainStatus, syncAppConfigsToRemote },
+        protectedApps: {
+          addDomainToRemote,
+          syncAppCustomDomainStatus,
+          syncAppConfigsToRemote,
+          deleteDomainFromRemote,
+          deleteRemoteAppConfigs,
+        },
       },
     },
   ]: RouterInitArgs<T>
@@ -108,4 +114,62 @@ export default function applicationProtectedAppMetadataRoutes<T extends AuthedRo
       return next();
     }
   );
+
+  router.delete(
+    `${customDomainsPathname}/:domain`,
+    koaGuard({
+      params: z.object({
+        ...params,
+        domain: z.string(),
+      }),
+      status: [204, 404],
+    }),
+    async (ctx, next) => {
+      const { id, domain } = ctx.guard.params;
+
+      const { protectedAppMetadata, oidcClientMetadata } = await findApplicationById(id);
+
+      const domainObject = protectedAppMetadata?.customDomains?.find(
+        ({ domain: domainName }) => domainName === domain
+      );
+
+      assertThat(
+        protectedAppMetadata && domainObject,
+        new RequestError({
+          code: 'application.custom_domain_not_found',
+          status: 404,
+        })
+      );
+
+      // Remove domain from Cloudflare
+      if (domainObject.cloudflareData?.id) {
+        await deleteDomainFromRemote(domainObject.cloudflareData.id);
+      }
+
+      // Remove site configs
+      await deleteRemoteAppConfigs(domain);
+
+      await updateApplicationById(id, {
+        oidcClientMetadata: {
+          ...oidcClientMetadata,
+          redirectUris: oidcClientMetadata.redirectUris.filter(
+            (uri) => uri !== `https://${domain}/callback`
+          ),
+          postLogoutRedirectUris: oidcClientMetadata.postLogoutRedirectUris.filter(
+            (uri) => uri !== `https://${domain}`
+          ),
+        },
+        protectedAppMetadata: {
+          ...protectedAppMetadata,
+          customDomains: protectedAppMetadata.customDomains?.filter(
+            ({ domain: domainName }) => domainName !== domain
+          ),
+        },
+      });
+
+      ctx.status = 204;
+
+      return next();
+    }
+  );
 }
diff --git a/packages/phrases/src/locales/de/errors/application.ts b/packages/phrases/src/locales/de/errors/application.ts
index d51a3a4c7..d6c38b197 100644
--- a/packages/phrases/src/locales/de/errors/application.ts
+++ b/packages/phrases/src/locales/de/errors/application.ts
@@ -23,6 +23,8 @@ const application = {
     'The subdomain of Protected application is already in use.',
   /** UNTRANSLATED */
   invalid_subdomain: 'Invalid subdomain.',
+  /** UNTRANSLATED */
+  custom_domain_not_found: 'Custom domain not found.',
 };
 
 export default Object.freeze(application);
diff --git a/packages/phrases/src/locales/en/errors/application.ts b/packages/phrases/src/locales/en/errors/application.ts
index ba295f358..d382787fc 100644
--- a/packages/phrases/src/locales/en/errors/application.ts
+++ b/packages/phrases/src/locales/en/errors/application.ts
@@ -15,6 +15,7 @@ const application = {
   protected_application_subdomain_exists:
     'The subdomain of Protected application is already in use.',
   invalid_subdomain: 'Invalid subdomain.',
+  custom_domain_not_found: 'Custom domain not found.',
 };
 
 export default Object.freeze(application);
diff --git a/packages/phrases/src/locales/es/errors/application.ts b/packages/phrases/src/locales/es/errors/application.ts
index 7a7a313a4..d35fe4cc2 100644
--- a/packages/phrases/src/locales/es/errors/application.ts
+++ b/packages/phrases/src/locales/es/errors/application.ts
@@ -23,6 +23,8 @@ const application = {
     'The subdomain of Protected application is already in use.',
   /** UNTRANSLATED */
   invalid_subdomain: 'Invalid subdomain.',
+  /** UNTRANSLATED */
+  custom_domain_not_found: 'Custom domain not found.',
 };
 
 export default Object.freeze(application);
diff --git a/packages/phrases/src/locales/fr/errors/application.ts b/packages/phrases/src/locales/fr/errors/application.ts
index d182eb9c0..1b9b47fdd 100644
--- a/packages/phrases/src/locales/fr/errors/application.ts
+++ b/packages/phrases/src/locales/fr/errors/application.ts
@@ -24,6 +24,8 @@ const application = {
     'The subdomain of Protected application is already in use.',
   /** UNTRANSLATED */
   invalid_subdomain: 'Invalid subdomain.',
+  /** UNTRANSLATED */
+  custom_domain_not_found: 'Custom domain not found.',
 };
 
 export default Object.freeze(application);
diff --git a/packages/phrases/src/locales/it/errors/application.ts b/packages/phrases/src/locales/it/errors/application.ts
index 24c567712..70cf9c9f4 100644
--- a/packages/phrases/src/locales/it/errors/application.ts
+++ b/packages/phrases/src/locales/it/errors/application.ts
@@ -24,6 +24,8 @@ const application = {
     'The subdomain of Protected application is already in use.',
   /** UNTRANSLATED */
   invalid_subdomain: 'Invalid subdomain.',
+  /** UNTRANSLATED */
+  custom_domain_not_found: 'Custom domain not found.',
 };
 
 export default Object.freeze(application);
diff --git a/packages/phrases/src/locales/ja/errors/application.ts b/packages/phrases/src/locales/ja/errors/application.ts
index 443f6df73..7e31ab8e5 100644
--- a/packages/phrases/src/locales/ja/errors/application.ts
+++ b/packages/phrases/src/locales/ja/errors/application.ts
@@ -23,6 +23,8 @@ const application = {
     'The subdomain of Protected application is already in use.',
   /** UNTRANSLATED */
   invalid_subdomain: 'Invalid subdomain.',
+  /** UNTRANSLATED */
+  custom_domain_not_found: 'Custom domain not found.',
 };
 
 export default Object.freeze(application);
diff --git a/packages/phrases/src/locales/ko/errors/application.ts b/packages/phrases/src/locales/ko/errors/application.ts
index 445b5f874..8ac1edd1f 100644
--- a/packages/phrases/src/locales/ko/errors/application.ts
+++ b/packages/phrases/src/locales/ko/errors/application.ts
@@ -22,6 +22,8 @@ const application = {
     'The subdomain of Protected application is already in use.',
   /** UNTRANSLATED */
   invalid_subdomain: 'Invalid subdomain.',
+  /** UNTRANSLATED */
+  custom_domain_not_found: 'Custom domain not found.',
 };
 
 export default Object.freeze(application);
diff --git a/packages/phrases/src/locales/pl-pl/errors/application.ts b/packages/phrases/src/locales/pl-pl/errors/application.ts
index a66bc7eb1..fbca65d91 100644
--- a/packages/phrases/src/locales/pl-pl/errors/application.ts
+++ b/packages/phrases/src/locales/pl-pl/errors/application.ts
@@ -22,6 +22,8 @@ const application = {
     'The subdomain of Protected application is already in use.',
   /** UNTRANSLATED */
   invalid_subdomain: 'Invalid subdomain.',
+  /** UNTRANSLATED */
+  custom_domain_not_found: 'Custom domain not found.',
 };
 
 export default Object.freeze(application);
diff --git a/packages/phrases/src/locales/pt-br/errors/application.ts b/packages/phrases/src/locales/pt-br/errors/application.ts
index 53626750a..29f161ecb 100644
--- a/packages/phrases/src/locales/pt-br/errors/application.ts
+++ b/packages/phrases/src/locales/pt-br/errors/application.ts
@@ -23,6 +23,8 @@ const application = {
     'The subdomain of Protected application is already in use.',
   /** UNTRANSLATED */
   invalid_subdomain: 'Invalid subdomain.',
+  /** UNTRANSLATED */
+  custom_domain_not_found: 'Custom domain not found.',
 };
 
 export default Object.freeze(application);
diff --git a/packages/phrases/src/locales/pt-pt/errors/application.ts b/packages/phrases/src/locales/pt-pt/errors/application.ts
index ee23fb35f..2a2231ac8 100644
--- a/packages/phrases/src/locales/pt-pt/errors/application.ts
+++ b/packages/phrases/src/locales/pt-pt/errors/application.ts
@@ -23,6 +23,8 @@ const application = {
     'The subdomain of Protected application is already in use.',
   /** UNTRANSLATED */
   invalid_subdomain: 'Invalid subdomain.',
+  /** UNTRANSLATED */
+  custom_domain_not_found: 'Custom domain not found.',
 };
 
 export default Object.freeze(application);
diff --git a/packages/phrases/src/locales/ru/errors/application.ts b/packages/phrases/src/locales/ru/errors/application.ts
index dcb1e43a2..f36f69da2 100644
--- a/packages/phrases/src/locales/ru/errors/application.ts
+++ b/packages/phrases/src/locales/ru/errors/application.ts
@@ -24,6 +24,8 @@ const application = {
     'The subdomain of Protected application is already in use.',
   /** UNTRANSLATED */
   invalid_subdomain: 'Invalid subdomain.',
+  /** UNTRANSLATED */
+  custom_domain_not_found: 'Custom domain not found.',
 };
 
 export default Object.freeze(application);
diff --git a/packages/phrases/src/locales/tr-tr/errors/application.ts b/packages/phrases/src/locales/tr-tr/errors/application.ts
index b38c6e5eb..0df264439 100644
--- a/packages/phrases/src/locales/tr-tr/errors/application.ts
+++ b/packages/phrases/src/locales/tr-tr/errors/application.ts
@@ -22,6 +22,8 @@ const application = {
     'The subdomain of Protected application is already in use.',
   /** UNTRANSLATED */
   invalid_subdomain: 'Invalid subdomain.',
+  /** UNTRANSLATED */
+  custom_domain_not_found: 'Custom domain not found.',
 };
 
 export default Object.freeze(application);
diff --git a/packages/phrases/src/locales/zh-cn/errors/application.ts b/packages/phrases/src/locales/zh-cn/errors/application.ts
index b10c4c028..8a0551378 100644
--- a/packages/phrases/src/locales/zh-cn/errors/application.ts
+++ b/packages/phrases/src/locales/zh-cn/errors/application.ts
@@ -21,6 +21,8 @@ const application = {
     'The subdomain of Protected application is already in use.',
   /** UNTRANSLATED */
   invalid_subdomain: 'Invalid subdomain.',
+  /** UNTRANSLATED */
+  custom_domain_not_found: 'Custom domain not found.',
 };
 
 export default Object.freeze(application);
diff --git a/packages/phrases/src/locales/zh-hk/errors/application.ts b/packages/phrases/src/locales/zh-hk/errors/application.ts
index be01213ca..9361a19bd 100644
--- a/packages/phrases/src/locales/zh-hk/errors/application.ts
+++ b/packages/phrases/src/locales/zh-hk/errors/application.ts
@@ -21,6 +21,8 @@ const application = {
     'The subdomain of Protected application is already in use.',
   /** UNTRANSLATED */
   invalid_subdomain: 'Invalid subdomain.',
+  /** UNTRANSLATED */
+  custom_domain_not_found: 'Custom domain not found.',
 };
 
 export default Object.freeze(application);
diff --git a/packages/phrases/src/locales/zh-tw/errors/application.ts b/packages/phrases/src/locales/zh-tw/errors/application.ts
index 63b88fb4c..162b6fbb8 100644
--- a/packages/phrases/src/locales/zh-tw/errors/application.ts
+++ b/packages/phrases/src/locales/zh-tw/errors/application.ts
@@ -21,6 +21,8 @@ const application = {
     'The subdomain of Protected application is already in use.',
   /** UNTRANSLATED */
   invalid_subdomain: 'Invalid subdomain.',
+  /** UNTRANSLATED */
+  custom_domain_not_found: 'Custom domain not found.',
 };
 
 export default Object.freeze(application);