diff --git a/cli/js/compiler.ts b/cli/js/compiler.ts
index 6cd5a6590f..79d517df27 100644
--- a/cli/js/compiler.ts
+++ b/cli/js/compiler.ts
@@ -140,7 +140,7 @@ async function tsCompilerOnMessage({
       const resolvedRootModules = await processImports(
         rootNames.map(rootName => [rootName, rootName]),
         undefined,
-        host.getCompilationSettings().checkJs
+        bundle || host.getCompilationSettings().checkJs
       );
 
       let emitSkipped = true;
@@ -208,27 +208,46 @@ async function tsCompilerOnMessage({
         ? rootName
         : resolveModules([rootName])[0];
 
+      // if there are options, convert them into TypeScript compiler options,
+      // and resolve any external file references
+      let convertedOptions: ts.CompilerOptions | undefined;
+      let additionalFiles: string[] | undefined;
+      if (options) {
+        const result = convertCompilerOptions(options);
+        convertedOptions = result.options;
+        additionalFiles = result.files;
+      }
+
+      const checkJsImports =
+        bundle || (convertedOptions && convertedOptions.checkJs);
+
       // recursively process imports, loading each file into memory.  If there
       // are sources, these files are pulled out of the there, otherwise the
       // files are retrieved from the privileged side
       const rootNames = sources
-        ? processLocalImports(sources, [[resolvedRootName, resolvedRootName]])
-        : await processImports([[resolvedRootName, resolvedRootName]]);
-
-      // if there are options, convert them into TypeScript compiler options,
-      // and resolve any external file references
-      let convertedOptions: ts.CompilerOptions | undefined;
-      if (options) {
-        const result = convertCompilerOptions(options);
-        convertedOptions = result.options;
-        if (result.files) {
-          // any files supplied in the configuration are resolved externally,
-          // even if sources are provided
-          const resolvedNames = resolveModules(result.files);
-          rootNames.push(
-            ...(await processImports(resolvedNames.map(rn => [rn, rn])))
+        ? processLocalImports(
+            sources,
+            [[resolvedRootName, resolvedRootName]],
+            undefined,
+            checkJsImports
+          )
+        : await processImports(
+            [[resolvedRootName, resolvedRootName]],
+            undefined,
+            checkJsImports
           );
-        }
+
+      if (additionalFiles) {
+        // any files supplied in the configuration are resolved externally,
+        // even if sources are provided
+        const resolvedNames = resolveModules(additionalFiles);
+        rootNames.push(
+          ...(await processImports(
+            resolvedNames.map(rn => [rn, rn]),
+            undefined,
+            checkJsImports
+          ))
+        );
       }
 
       const state: WriteFileState = {
diff --git a/cli/js/compiler_api_test.ts b/cli/js/compiler_api_test.ts
index 64ba70afb7..fcca0a22b6 100644
--- a/cli/js/compiler_api_test.ts
+++ b/cli/js/compiler_api_test.ts
@@ -135,6 +135,15 @@ test(async function bundleApiConfig() {
   assert(!actual.includes(`random`));
 });
 
+test(async function bundleApiJsModules() {
+  const [diagnostics, actual] = await bundle("/foo.js", {
+    "/foo.js": `export * from "./bar.js";\n`,
+    "/bar.js": `export const bar = "bar";\n`
+  });
+  assert(diagnostics == null);
+  assert(actual.includes(`System.register("bar",`));
+});
+
 test(async function diagnosticsTest() {
   const [diagnostics] = await compile("/foo.ts", {
     "/foo.ts": `document.getElementById("foo");`
diff --git a/cli/js/compiler_host.ts b/cli/js/compiler_host.ts
index 78ed4889a7..585a7833ec 100644
--- a/cli/js/compiler_host.ts
+++ b/cli/js/compiler_host.ts
@@ -37,6 +37,7 @@ export interface ConfigureResponse {
 /** Options that need to be used when generating a bundle (either trusted or
  * runtime). */
 export const defaultBundlerOptions: ts.CompilerOptions = {
+  allowJs: true,
   inlineSourceMap: false,
   module: ts.ModuleKind.System,
   outDir: undefined,
diff --git a/cli/js/compiler_imports.ts b/cli/js/compiler_imports.ts
index 6e8a6585df..903bcfe4dd 100644
--- a/cli/js/compiler_imports.ts
+++ b/cli/js/compiler_imports.ts
@@ -120,7 +120,7 @@ export function processLocalImports(
   sources: Record<string, string>,
   specifiers: Array<[string, string]>,
   referrer?: string,
-  checkJs = false
+  processJsImports = false
 ): string[] {
   if (!specifiers.length) {
     return [];
@@ -145,9 +145,9 @@ export function processLocalImports(
     if (!sourceFile.processed) {
       processLocalImports(
         sources,
-        sourceFile.imports(checkJs),
+        sourceFile.imports(processJsImports),
         sourceFile.url,
-        checkJs
+        processJsImports
       );
     }
   }
@@ -163,7 +163,7 @@ export function processLocalImports(
 export async function processImports(
   specifiers: Array<[string, string]>,
   referrer?: string,
-  checkJs = false
+  processJsImports = false
 ): Promise<string[]> {
   if (!specifiers.length) {
     return [];
@@ -179,9 +179,9 @@ export async function processImports(
     sourceFile.cache(specifiers[i][0], referrer);
     if (!sourceFile.processed) {
       await processImports(
-        sourceFile.imports(checkJs),
+        sourceFile.imports(processJsImports),
         sourceFile.url,
-        checkJs
+        processJsImports
       );
     }
   }
diff --git a/cli/js/compiler_sourcefile.ts b/cli/js/compiler_sourcefile.ts
index 23fefbf41e..cc7d4aa3eb 100644
--- a/cli/js/compiler_sourcefile.ts
+++ b/cli/js/compiler_sourcefile.ts
@@ -91,7 +91,7 @@ export class SourceFile {
   }
 
   /** Process the imports for the file and return them. */
-  imports(checkJs: boolean): Array<[string, string]> {
+  imports(processJsImports: boolean): Array<[string, string]> {
     if (this.processed) {
       throw new Error("SourceFile has already been processed.");
     }
@@ -134,7 +134,7 @@ export class SourceFile {
       }
     } else if (
       !(
-        !checkJs &&
+        !processJsImports &&
         (this.mediaType === MediaType.JavaScript ||
           this.mediaType === MediaType.JSX)
       )
diff --git a/cli/tests/integration_tests.rs b/cli/tests/integration_tests.rs
index d7e8077937..a475e9111a 100644
--- a/cli/tests/integration_tests.rs
+++ b/cli/tests/integration_tests.rs
@@ -436,6 +436,36 @@ fn bundle_tla() {
   assert_eq!(output.stderr, b"");
 }
 
+#[test]
+fn bundle_js() {
+  use tempfile::TempDir;
+
+  // First we have to generate a bundle of some module that has exports.
+  let mod6 = util::root_path().join("cli/tests/subdir/mod6.js");
+  assert!(mod6.is_file());
+  let t = TempDir::new().expect("tempdir fail");
+  let bundle = t.path().join("mod6.bundle.js");
+  let mut deno = util::deno_cmd()
+    .current_dir(util::root_path())
+    .arg("bundle")
+    .arg(mod6)
+    .arg(&bundle)
+    .spawn()
+    .expect("failed to spawn script");
+  let status = deno.wait().expect("failed to wait for the child process");
+  assert!(status.success());
+  assert!(bundle.is_file());
+
+  let output = util::deno_cmd()
+    .current_dir(util::root_path())
+    .arg("run")
+    .arg(&bundle)
+    .output()
+    .expect("failed to spawn script");
+  // check that nothing went to stderr
+  assert_eq!(output.stderr, b"");
+}
+
 #[test]
 fn repl_test_console_log() {
   let (out, err, code) = util::run_and_collect_output(