diff --git a/src/compiler/emitter.ts b/src/compiler/emitter.ts
index e1c59b9eea0..1b307920c55 100644
--- a/src/compiler/emitter.ts
+++ b/src/compiler/emitter.ts
@@ -212,6 +212,7 @@ namespace ts {
         } = comments;
 
         let currentSourceFile: SourceFile;
+        let statementOffset: number;  // We cache the index of first non prologue so we don't have to recalculate it multiple times like in emitBodyInDirect
         let nodeIdToGeneratedName: string[]; // Map of generated names for specific nodes.
         let autoGeneratedIdToGeneratedName: string[]; // Map of generated names for temp and loop variables.
         let generatedNames: Map<string>; // Set of names generated by the NameGenerator.
@@ -275,6 +276,7 @@ namespace ts {
             const previousWriter = writer;
             setWriter(output);
             emitShebangIfNeeded(bundle);
+            emitPrologueDirectivesIfNeeded(bundle);
             emitHelpersIndirect(bundle);
             for (const sourceFile of bundle.sourceFiles) {
                 print(EmitHint.SourceFile, sourceFile, sourceFile);
@@ -287,6 +289,7 @@ namespace ts {
             const previousWriter = writer;
             setWriter(output);
             emitShebangIfNeeded(sourceFile);
+            emitPrologueDirectivesIfNeeded(sourceFile);
             print(EmitHint.SourceFile, sourceFile, sourceFile);
             reset();
             writer = previousWriter;
@@ -309,6 +312,7 @@ namespace ts {
 
         function setSourceFile(sourceFile: SourceFile) {
             currentSourceFile = sourceFile;
+            statementOffset = getIndexOfFirstNonPrologueDirectives(sourceFile.statements);
             comments.setSourceFile(sourceFile);
             if (onSetSourceFile) {
                 onSetSourceFile(sourceFile);
@@ -733,7 +737,11 @@ namespace ts {
         }
 
         function emitBodyIndirect(node: Node, elements: NodeArray<Node>, emitCallback: (node: Node) => void): void {
-            if (emitBodyWithDetachedComments) {
+            // If the node is a sourceFile and it has prologueDirective (statmentOffSet is not zero) that is synthesize
+            // We will need to emit detached comment here because emitPrologueDirective will not emit comments of such prologue directive
+            const shouldEmitDetachedComment = node.kind !== SyntaxKind.SourceFile ? true :
+                statementOffset === 0 || nodeIsSynthesized((node as SourceFile).statements[statementOffset - 1]);
+            if (emitBodyWithDetachedComments && shouldEmitDetachedComment) {
                 emitBodyWithDetachedComments(node, elements, emitCallback);
             }
             else {
@@ -2058,7 +2066,6 @@ namespace ts {
 
         function emitSourceFileWorker(node: SourceFile) {
             const statements = node.statements;
-            const statementOffset = emitPrologueDirectives(statements);
             pushNameGenerationScope();
             emitHelpersIndirect(node);
             emitList(node, statements, ListFormat.MultiLine, statementOffset);
@@ -2075,13 +2082,20 @@ namespace ts {
          * Emits any prologue directives at the start of a Statement list, returning the
          * number of prologue directives written to the output.
          */
-        function emitPrologueDirectives(statements: Node[], startWithNewLine?: boolean): number {
+        function emitPrologueDirectives(statements: Node[], startWithNewLine?: boolean, seenPrologueDirectives?: Map<String>): number {
             for (let i = 0; i < statements.length; i++) {
-                if (isPrologueDirective(statements[i])) {
-                    if (startWithNewLine || i > 0) {
-                        writeLine();
+                const statement = statements[i];
+                if (isPrologueDirective(statement)) {
+                    const shouldEmitPrologueDirective = seenPrologueDirectives ? !seenPrologueDirectives.has(statement.expression.text) : true;
+                    if (shouldEmitPrologueDirective) {
+                        if (startWithNewLine || i > 0) {
+                            writeLine();
+                        }
+                        emit(statement);
+                        if (seenPrologueDirectives) {
+                            seenPrologueDirectives.set(statement.expression.text, statement.expression.text);
+                        }
                     }
-                    emit(statements[i]);
                 }
                 else {
                     // return index of the first non prologue directive
@@ -2092,9 +2106,19 @@ namespace ts {
             return statements.length;
         }
 
-        //
-        // Helpers
-        //
+        function emitPrologueDirectivesIfNeeded(sourceFileOrBundle: Bundle | SourceFile) {
+            if (sourceFileOrBundle.kind === SyntaxKind.SourceFile) {
+                setSourceFile(sourceFileOrBundle as SourceFile);
+                emitPrologueDirectives((sourceFileOrBundle as SourceFile).statements);
+            }
+            else {
+                const seenProgolueDirectives = createMap<String>();
+                for (const sourceFile of (sourceFileOrBundle as Bundle).sourceFiles) {
+                    setSourceFile(sourceFile);
+                    emitPrologueDirectives(sourceFile.statements, /*startWithNewLine*/ true, seenProgolueDirectives);
+                }
+            }
+        }
 
         function emitShebangIfNeeded(sourceFileOrBundle: Bundle | SourceFile) {
             if (sourceFileOrBundle.kind === SyntaxKind.SourceFile) {
@@ -2119,6 +2143,19 @@ namespace ts {
             }
         }
 
+        //
+        // Helpers
+        //
+
+        function getIndexOfFirstNonPrologueDirectives(statements: Statement[]): number {
+            for (let i = 0; i < statements.length; i++) {
+                if (!isPrologueDirective(statements[i])) {
+                    return i;
+                }
+            }
+            return statements.length;
+        }
+
         function emitModifiers(node: Node, modifiers: NodeArray<Modifier>) {
             if (modifiers && modifiers.length) {
                 emitList(node, modifiers, ListFormat.Modifiers);