diff --git a/src/compiler/program.ts b/src/compiler/program.ts
index a3d6de8e2f7fc..42c5973d1fb0c 100644
--- a/src/compiler/program.ts
+++ b/src/compiler/program.ts
@@ -1359,7 +1359,7 @@ namespace ts {
             }
 
             // If the emit is enabled make sure that every output file is unique and not overwriting any of the input files
-            if (!options.noEmit) {
+            if (!options.noEmit && !options.suppressOutputPathCheck) {
                 const emitHost = getEmitHost();
                 const emitFilesSeen = createFileMap<boolean>(!host.useCaseSensitiveFileNames() ? key => key.toLocaleLowerCase() : undefined);
                 forEachExpectedEmitFile(emitHost, (emitFileNames, sourceFiles, isBundledEmit) => {
diff --git a/src/compiler/types.ts b/src/compiler/types.ts
index b21b6fd59ed87..ce3dbe7f4598b 100644
--- a/src/compiler/types.ts
+++ b/src/compiler/types.ts
@@ -2438,6 +2438,8 @@ namespace ts {
 
         // Skip checking lib.d.ts to help speed up tests.
         /* @internal */ skipDefaultLibCheck?: boolean;
+        // Do not perform validation of output file name in transpile scenarios
+        /* @internal */ suppressOutputPathCheck?: boolean;
 
         [option: string]: string | number | boolean;
     }
diff --git a/src/services/services.ts b/src/services/services.ts
index 28f7f8488355e..37f54de5c3c6e 100644
--- a/src/services/services.ts
+++ b/src/services/services.ts
@@ -1875,6 +1875,9 @@ namespace ts {
 
         options.isolatedModules = true;
 
+        // transpileModule does not write anything to disk so there is no need to verify that there are no conflicts between input and output paths. 
+        options.suppressOutputPathCheck = true;
+
         // Filename can be non-ts file.
         options.allowNonTsExtensions = true;
 
diff --git a/tests/cases/unittests/transpile.ts b/tests/cases/unittests/transpile.ts
index d9fdaeb32ecc7..6f46bb53405c5 100644
--- a/tests/cases/unittests/transpile.ts
+++ b/tests/cases/unittests/transpile.ts
@@ -291,5 +291,14 @@ var x = 0;`,
                 options: { compilerOptions: { jsx: JsxEmit.React, newLine: NewLineKind.LineFeed } }
             })
         });
+        it("transpile .js files", () => {
+            const input = "const a = 10;";
+            const output = `"use strict";\nvar a = 10;\n`;
+            test(input, {
+                expectedOutput: output,
+                options: { compilerOptions: { newLine: NewLineKind.LineFeed, module: ModuleKind.CommonJS }, fileName: "input.js", reportDiagnostics: true },
+                expectedDiagnosticCodes: []
+            });
+        })
     });
 }