diff --git a/src/compiler/core.ts b/src/compiler/core.ts
index 6035f9898ce..22cafc034b4 100644
--- a/src/compiler/core.ts
+++ b/src/compiler/core.ts
@@ -723,8 +723,10 @@ namespace ts {
      */
     export const supportedTypeScriptExtensions = ["ts", "tsx", "d.ts"];
 
-    const extensionsToRemove = ["d.ts", "ts", "js", "tsx", "jsx"];
-    export function removeFileExtension(path: string): string {
+    export function removeFileExtension(path: string, supportedExtensions: string[]): string {
+        // Sort the extensions in descending order of their length
+        let extensionsToRemove = supportedExtensions.slice(0, supportedExtensions.length) // Get duplicate array
+            .sort((ext1, ext2) => compareValues(ext2.length, ext1.length)); // Sort in descending order of extension length
         for (let ext of extensionsToRemove) {
             if (fileExtensionIs(path, ext)) {
                 return path.substr(0, path.length - ext.length - 1);
diff --git a/src/compiler/declarationEmitter.ts b/src/compiler/declarationEmitter.ts
index 4c0c6d20ad0..9e8e366aaac 100644
--- a/src/compiler/declarationEmitter.ts
+++ b/src/compiler/declarationEmitter.ts
@@ -1605,7 +1605,7 @@ namespace ts {
                 ? referencedFile.fileName // Declaration file, use declaration file name
                 : shouldEmitToOwnFile(referencedFile, compilerOptions)
                     ? getOwnEmitOutputFilePath(referencedFile, host, ".d.ts") // Own output file so get the .d.ts file
-                    : removeFileExtension(compilerOptions.outFile || compilerOptions.out) + ".d.ts"; // Global out file
+                    : removeFileExtension(compilerOptions.outFile || compilerOptions.out, getExtensionsToRemoveForEmitPath(compilerOptions)) + ".d.ts"; // Global out file
 
             declFileName = getRelativePathToDirectoryOrUrl(
                 getDirectoryPath(normalizeSlashes(jsFilePath)),
@@ -1626,7 +1626,8 @@ namespace ts {
         if (!emitDeclarationResult.reportedDeclarationError) {
             let declarationOutput = emitDeclarationResult.referencePathsOutput
                 + getDeclarationOutput(emitDeclarationResult.synchronousDeclarationOutput, emitDeclarationResult.moduleElementDeclarationEmitInfo);
-            writeFile(host, diagnostics, removeFileExtension(jsFilePath) + ".d.ts", declarationOutput, host.getCompilerOptions().emitBOM);
+            let compilerOptions = host.getCompilerOptions();
+            writeFile(host, diagnostics, removeFileExtension(jsFilePath, getExtensionsToRemoveForEmitPath(compilerOptions)) + ".d.ts", declarationOutput, compilerOptions.emitBOM);
         }
 
         function getDeclarationOutput(synchronousDeclarationOutput: string, moduleElementDeclarationEmitInfo: ModuleElementDeclarationEmitInfo[]) {
diff --git a/src/compiler/utilities.ts b/src/compiler/utilities.ts
index 00efbe9616e..dc43b837c7c 100644
--- a/src/compiler/utilities.ts
+++ b/src/compiler/utilities.ts
@@ -1748,14 +1748,19 @@ namespace ts {
         };
     }
 
+    export function getExtensionsToRemoveForEmitPath(compilerOptons: CompilerOptions) {
+        return getSupportedExtensions(compilerOptons).concat("jsx", "js");
+    }
+
     export function getOwnEmitOutputFilePath(sourceFile: SourceFile, host: EmitHost, extension: string) {
         let compilerOptions = host.getCompilerOptions();
         let emitOutputFilePathWithoutExtension: string;
         if (compilerOptions.outDir) {
-            emitOutputFilePathWithoutExtension = removeFileExtension(getSourceFilePathInNewDir(sourceFile, host, compilerOptions.outDir));
+            emitOutputFilePathWithoutExtension = removeFileExtension(getSourceFilePathInNewDir(sourceFile, host, compilerOptions.outDir),
+                getExtensionsToRemoveForEmitPath(compilerOptions));
         }
         else {
-            emitOutputFilePathWithoutExtension = removeFileExtension(sourceFile.fileName);
+            emitOutputFilePathWithoutExtension = removeFileExtension(sourceFile.fileName, getExtensionsToRemoveForEmitPath(compilerOptions));
         }
 
         return emitOutputFilePathWithoutExtension + extension;
diff --git a/src/harness/harness.ts b/src/harness/harness.ts
index 451bb4adfc6..4ebc1976217 100644
--- a/src/harness/harness.ts
+++ b/src/harness/harness.ts
@@ -1187,7 +1187,7 @@ namespace Harness {
                             sourceFileName = outFile;
                         }
 
-                        let dTsFileName = ts.removeFileExtension(sourceFileName) + ".d.ts";
+                        let dTsFileName = ts.removeFileExtension(sourceFileName, ts.getExtensionsToRemoveForEmitPath(options)) + ".d.ts";
 
                         return ts.forEach(result.declFilesCode, declFile => declFile.fileName === dTsFileName ? declFile : undefined);
                     }
diff --git a/src/harness/projectsRunner.ts b/src/harness/projectsRunner.ts
index 39c9a458e9c..cd099279fa8 100644
--- a/src/harness/projectsRunner.ts
+++ b/src/harness/projectsRunner.ts
@@ -356,17 +356,17 @@ class ProjectRunner extends RunnerBase {
                     if (compilerOptions.outDir) {
                         let sourceFilePath = ts.getNormalizedAbsolutePath(sourceFile.fileName, compilerResult.program.getCurrentDirectory());
                         sourceFilePath = sourceFilePath.replace(compilerResult.program.getCommonSourceDirectory(), "");
-                        emitOutputFilePathWithoutExtension = ts.removeFileExtension(ts.combinePaths(compilerOptions.outDir, sourceFilePath));
+                        emitOutputFilePathWithoutExtension = ts.removeFileExtension(ts.combinePaths(compilerOptions.outDir, sourceFilePath), ts.getExtensionsToRemoveForEmitPath(compilerOptions));
                     }
                     else {
-                        emitOutputFilePathWithoutExtension = ts.removeFileExtension(sourceFile.fileName);
+                        emitOutputFilePathWithoutExtension = ts.removeFileExtension(sourceFile.fileName, ts.getExtensionsToRemoveForEmitPath(compilerOptions));
                     }
 
                     let outputDtsFileName = emitOutputFilePathWithoutExtension + ".d.ts";
                     allInputFiles.unshift(findOutpuDtsFile(outputDtsFileName));
                 }
                 else {
-                    let outputDtsFileName = ts.removeFileExtension(compilerOptions.outFile || compilerOptions.out) + ".d.ts";
+                    let outputDtsFileName = ts.removeFileExtension(compilerOptions.outFile || compilerOptions.out, ts.getExtensionsToRemoveForEmitPath(compilerOptions)) + ".d.ts";
                     let outputDtsFile = findOutpuDtsFile(outputDtsFileName);
                     if (!ts.contains(allInputFiles, outputDtsFile)) {
                         allInputFiles.unshift(outputDtsFile);
diff --git a/src/harness/test262Runner.ts b/src/harness/test262Runner.ts
index 491c71a5839..1e95fc4ae74 100644
--- a/src/harness/test262Runner.ts
+++ b/src/harness/test262Runner.ts
@@ -37,7 +37,7 @@ class Test262BaselineRunner extends RunnerBase {
 
             before(() => {
                 let content = Harness.IO.readFile(filePath);
-                let testFilename = ts.removeFileExtension(filePath).replace(/\//g, "_") + ".test";
+                let testFilename = ts.removeFileExtension(filePath, ["js"]).replace(/\//g, "_") + ".test";
                 let testCaseContent = Harness.TestCaseParser.makeUnitsFromTest(content, testFilename);
 
                 let inputFiles = testCaseContent.testUnitData.map(unit => {
diff --git a/tests/cases/unittests/transpile.ts b/tests/cases/unittests/transpile.ts
index ca7d1faa4a9..95f7f443565 100644
--- a/tests/cases/unittests/transpile.ts
+++ b/tests/cases/unittests/transpile.ts
@@ -64,7 +64,7 @@ module ts {
             let transpileModuleResultWithSourceMap = transpileModule(input, transpileOptions);
             assert.isTrue(transpileModuleResultWithSourceMap.sourceMapText !== undefined);
             
-            let expectedSourceMapFileName = removeFileExtension(getBaseFileName(normalizeSlashes(transpileOptions.fileName))) + ".js.map";
+            let expectedSourceMapFileName = removeFileExtension(getBaseFileName(normalizeSlashes(transpileOptions.fileName)), ts.getExtensionsToRemoveForEmitPath(transpileOptions.compilerOptions)) + ".js.map";
             let expectedSourceMappingUrlLine = `//# sourceMappingURL=${expectedSourceMapFileName}`;
                         
             if (testSettings.expectedOutput !== undefined) {