diff --git a/src/compile-dts.ts b/src/compile-dts.ts
index b84c42c..db094a5 100644
--- a/src/compile-dts.ts
+++ b/src/compile-dts.ts
@@ -96,10 +96,14 @@ function changeExtensionToDts(fileName: string): string {
 function getDeclarationFiles(rootFiles: readonly string[], compilerOptions: ts.CompilerOptions): Map<string, string> {
 	// we must pass `declaration: true` and `noEmit: false` if we want to generate declaration files
 	// see https://github.com/microsoft/TypeScript/issues/24002#issuecomment-550549393
+	// also, we don't want to generate anything apart from declarations so that's why `emitDeclarationOnly: true` is here
+	// it allows to run the tool for projects with allowJs flag enabled to avoid errors like:
+	// error TS5055: Cannot write file '<filename>' because it would overwrite input file.
 	compilerOptions = {
 		...compilerOptions,
 		noEmit: false,
 		declaration: true,
+		emitDeclarationOnly: true,
 	};
 
 	const program = ts.createProgram(rootFiles, compilerOptions);
diff --git a/tests/e2e/test-cases/allow-js/config.ts b/tests/e2e/test-cases/allow-js/config.ts
new file mode 100644
index 0000000..f1fb1a8
--- /dev/null
+++ b/tests/e2e/test-cases/allow-js/config.ts
@@ -0,0 +1,5 @@
+import { TestCaseConfig } from '../../test-cases/test-case-config';
+
+const config: TestCaseConfig = {};
+
+export = config;
diff --git a/tests/e2e/test-cases/allow-js/hello.js b/tests/e2e/test-cases/allow-js/hello.js
new file mode 100644
index 0000000..4544e17
--- /dev/null
+++ b/tests/e2e/test-cases/allow-js/hello.js
@@ -0,0 +1,3 @@
+const hello = { test: 1 };
+
+export { hello }
diff --git a/tests/e2e/test-cases/allow-js/input.ts b/tests/e2e/test-cases/allow-js/input.ts
new file mode 100644
index 0000000..9e91fc8
--- /dev/null
+++ b/tests/e2e/test-cases/allow-js/input.ts
@@ -0,0 +1,5 @@
+import { hello } from "./hello.js";
+
+export function test() {
+	return hello
+}
diff --git a/tests/e2e/test-cases/allow-js/output.d.ts b/tests/e2e/test-cases/allow-js/output.d.ts
new file mode 100644
index 0000000..57c4d37
--- /dev/null
+++ b/tests/e2e/test-cases/allow-js/output.d.ts
@@ -0,0 +1,5 @@
+export declare function test(): {
+	test: number;
+};
+
+export {};
diff --git a/tests/e2e/test-cases/allow-js/tsconfig.json b/tests/e2e/test-cases/allow-js/tsconfig.json
new file mode 100644
index 0000000..bf3a541
--- /dev/null
+++ b/tests/e2e/test-cases/allow-js/tsconfig.json
@@ -0,0 +1,6 @@
+{
+	"extends": "../tsconfig.json",
+	"compilerOptions": {
+		"allowJs": true
+	}
+}