diff --git a/packages/compiler-cli/ngcc/src/packages/entry_point_bundle.ts b/packages/compiler-cli/ngcc/src/packages/entry_point_bundle.ts
index dec8293a4e..72768725a5 100644
--- a/packages/compiler-cli/ngcc/src/packages/entry_point_bundle.ts
+++ b/packages/compiler-cli/ngcc/src/packages/entry_point_bundle.ts
@@ -73,16 +73,20 @@ export function makeEntryPointBundle(
 function computePotentialDtsFilesFromJsFiles(
     fs: FileSystem, srcProgram: ts.Program, formatPath: AbsoluteFsPath,
     typingsPath: AbsoluteFsPath) {
-  const relativePath = fs.relative(fs.dirname(formatPath), fs.dirname(typingsPath));
+  const formatRoot = fs.dirname(formatPath);
+  const typingsRoot = fs.dirname(typingsPath);
   const additionalFiles: AbsoluteFsPath[] = [];
   for (const sf of srcProgram.getSourceFiles()) {
     if (!sf.fileName.endsWith('.js')) {
       continue;
     }
-    const dtsPath = fs.resolve(
-        fs.dirname(sf.fileName), relativePath, fs.basename(sf.fileName, '.js') + '.d.ts');
-    if (fs.exists(dtsPath)) {
-      additionalFiles.push(dtsPath);
+
+    // Given a source file at e.g. `esm2015/src/some/nested/index.js`, try to resolve the
+    // declaration file under the typings root in `src/some/nested/index.d.ts`.
+    const mirroredDtsPath =
+        fs.resolve(typingsRoot, fs.relative(formatRoot, sf.fileName.replace(/\.js$/, '.d.ts')));
+    if (fs.exists(mirroredDtsPath)) {
+      additionalFiles.push(mirroredDtsPath);
     }
   }
   return additionalFiles;
diff --git a/packages/compiler-cli/ngcc/test/packages/entry_point_bundle_spec.ts b/packages/compiler-cli/ngcc/test/packages/entry_point_bundle_spec.ts
index 5d43ef0031..285a219e6f 100644
--- a/packages/compiler-cli/ngcc/test/packages/entry_point_bundle_spec.ts
+++ b/packages/compiler-cli/ngcc/test/packages/entry_point_bundle_spec.ts
@@ -128,6 +128,26 @@ runInEachFileSystem(() => {
           name: _('/node_modules/other/es2015/public_api.js'),
           contents: 'export class OtherClass {};'
         },
+
+        // Mimic an AFP package with declaration files in a different tree than the sources
+        {name: _('/node_modules/internal/index.d.ts'), contents: 'export * from "./src/index";'},
+        {name: _('/node_modules/internal/src/index.d.ts'), contents: ''},
+        {
+          name: _('/node_modules/internal/src/internal.d.ts'),
+          contents: 'export declare function internal();'
+        },
+        {
+          name: _('/node_modules/internal/esm2015/index.js'),
+          contents: 'export * from "./src/index";'
+        },
+        {
+          name: _('/node_modules/internal/esm2015/src/index.js'),
+          contents: 'import {Internal} from "./internal";'
+        },
+        {
+          name: _('/node_modules/internal/esm2015/src/internal.js'),
+          contents: 'export function internal();'
+        },
       ]);
     }
 
@@ -203,6 +223,29 @@ runInEachFileSystem(() => {
              .toContain(absoluteFrom('/node_modules/test/internal.d.ts'));
        });
 
+    it('should include equivalently named, internally imported, src files in the typings program, if `mirrorDtsFromSrc` is true',
+       () => {
+         setupMockFileSystem();
+         const fs = getFileSystem();
+         const entryPoint: EntryPoint = {
+           name: 'internal',
+           packageJson: {name: 'internal'},
+           package: absoluteFrom('/node_modules/internal'),
+           path: absoluteFrom('/node_modules/internal'),
+           typings: absoluteFrom('/node_modules/internal/index.d.ts'),
+           compiledByAngular: true,
+           ignoreMissingDependencies: false,
+           generateDeepReexports: false,
+         };
+         const esm5bundle = makeEntryPointBundle(
+             fs, entryPoint, './esm2015/index.js', false, 'esm2015', /* transformDts */ true,
+             /* pathMappings */ undefined, /* mirrorDtsFromSrc */ true);
+         expect(esm5bundle.src.program.getSourceFiles().map(sf => sf.fileName))
+             .toContain(absoluteFrom('/node_modules/internal/esm2015/src/internal.js'));
+         expect(esm5bundle.dts !.program.getSourceFiles().map(sf => sf.fileName))
+             .toContain(absoluteFrom('/node_modules/internal/src/internal.d.ts'));
+       });
+
     it('should ignore, internally imported, src files in the typings program, if `mirrorDtsFromSrc` is false',
        () => {
          setupMockFileSystem();