diff --git a/packages/compiler-cli/src/ngtsc/annotations/src/metadata.ts b/packages/compiler-cli/src/ngtsc/annotations/src/metadata.ts
index e0ac434c4b..36701e189d 100644
--- a/packages/compiler-cli/src/ngtsc/annotations/src/metadata.ts
+++ b/packages/compiler-cli/src/ngtsc/annotations/src/metadata.ts
@@ -39,8 +39,13 @@ export function generateSetClassMetadataCall(
   }
   const ngClassDecorators =
       classDecorators.filter(dec => isAngularDecorator(dec, isCore))
-          .map(
-              (decorator: Decorator) => decoratorToMetadata(decorator, annotateForClosureCompiler));
+          .map(decorator => decoratorToMetadata(decorator, annotateForClosureCompiler))
+          // Since the `setClassMetadata` call is intended to be emitted after the class
+          // declaration, we have to strip references to the existing identifiers or
+          // TypeScript might generate invalid code when it emits to JS. In particular
+          // this can break when emitting a class to ES5 which has a custom decorator
+          // and is referenced inside of its own metadata (see #39509 for more information).
+          .map(decorator => removeIdentifierReferences(decorator, id.text));
   if (ngClassDecorators.length === 0) {
     return null;
   }
@@ -166,3 +171,19 @@ function decoratorToMetadata(
 function isAngularDecorator(decorator: Decorator, isCore: boolean): boolean {
   return isCore || (decorator.import !== null && decorator.import.from === '@angular/core');
 }
+
+/**
+ * Recursively recreates all of the `Identifier` descendant nodes with a particular name inside
+ * of an AST node, thus removing any references to them. Useful if a particular node has to be t
+ * aken from one place any emitted to another one exactly as it has been written.
+ */
+function removeIdentifierReferences<T extends ts.Node>(node: T, name: string): T {
+  const result = ts.transform(
+      node, [context => root => ts.visitNode(root, function walk(current: ts.Node): ts.Node {
+        return ts.isIdentifier(current) && current.text === name ?
+            ts.createIdentifier(current.text) :
+            ts.visitEachChild(current, walk, context);
+      })]);
+
+  return result.transformed[0];
+}
diff --git a/packages/compiler-cli/test/compliance/r3_compiler_compliance_spec.ts b/packages/compiler-cli/test/compliance/r3_compiler_compliance_spec.ts
index 157b724db0..6241df64e3 100644
--- a/packages/compiler-cli/test/compliance/r3_compiler_compliance_spec.ts
+++ b/packages/compiler-cli/test/compliance/r3_compiler_compliance_spec.ts
@@ -8,6 +8,7 @@
 
 import {AttributeMarker} from '@angular/compiler/src/core';
 import {setup} from '@angular/compiler/test/aot/test_util';
+import * as ts from 'typescript';
 import {compile, expectEmit} from './mock_compile';
 
 
@@ -3313,5 +3314,46 @@ describe('compiler compliance', () => {
       const result = compile(files, angularFiles);
       expectEmit(result.source, MyAppDeclaration, 'Invalid component definition');
     });
+
+    it('should emit a valid setClassMetadata call in ES5 if a class with a custom decorator is referencing itself inside its own metadata',
+       () => {
+         const files = {
+           app: {
+             'spec.ts': `
+                import {Component, InjectionToken} from "@angular/core";
+
+                const token = new InjectionToken('token');
+
+                export function Custom() {
+                  return function(target: any) {};
+                }
+
+                @Custom()
+                @Component({
+                  template: '',
+                  providers: [{ provide: token, useExisting: Comp }],
+                })
+                export class Comp {}
+              `
+           }
+         };
+
+         // The setClassMetadata call should look like this.
+         const setClassMetadata = `
+            …
+            (function() {
+              i0.ɵsetClassMetadata(Comp, [{
+                type: Component,
+                args: [{
+                  template: '',
+                  providers: [{ provide: token, useExisting: Comp }],
+                }]
+              }], null, null);
+            })();
+          `;
+
+         const result = compile(files, angularFiles, {target: ts.ScriptTarget.ES5});
+         expectEmit(result.source, setClassMetadata, 'Incorrect setClassMetadata call');
+       });
   });
 });