diff --git a/src/compiler/emitter.ts b/src/compiler/emitter.ts
index 48718146ac6ad..0d2ffc4154d18 100644
--- a/src/compiler/emitter.ts
+++ b/src/compiler/emitter.ts
@@ -5493,7 +5493,7 @@ if (typeof __param !== "function") __param = function (paramIndex, decorator) {
                     paramEmitted = true;
                 }
 
-                if (isExternalModule(node)) {
+                if (isExternalModule(node) || compilerOptions.separateCompilation) {
                     if (languageVersion >= ScriptTarget.ES6) {
                         emitES6Module(node, startIndex);
                     }
diff --git a/tests/baselines/reference/separateCompilationPlainFile-AMD.errors.txt b/tests/baselines/reference/separateCompilationPlainFile-AMD.errors.txt
new file mode 100644
index 0000000000000..3605dc7f44e99
--- /dev/null
+++ b/tests/baselines/reference/separateCompilationPlainFile-AMD.errors.txt
@@ -0,0 +1,10 @@
+tests/cases/compiler/separateCompilationPlainFile-AMD.ts(2,1): error TS1208: Cannot compile non-external modules when the '--separateCompilation' flag is provided.
+
+
+==== tests/cases/compiler/separateCompilationPlainFile-AMD.ts (1 errors) ====
+    
+    declare function run(a: number): void;
+    ~~~~~~~
+!!! error TS1208: Cannot compile non-external modules when the '--separateCompilation' flag is provided.
+    run(1);
+    
\ No newline at end of file
diff --git a/tests/baselines/reference/separateCompilationPlainFile-AMD.js b/tests/baselines/reference/separateCompilationPlainFile-AMD.js
new file mode 100644
index 0000000000000..e3e9fc1eaeb89
--- /dev/null
+++ b/tests/baselines/reference/separateCompilationPlainFile-AMD.js
@@ -0,0 +1,10 @@
+//// [separateCompilationPlainFile-AMD.ts]
+
+declare function run(a: number): void;
+run(1);
+
+
+//// [separateCompilationPlainFile-AMD.js]
+define(["require", "exports"], function (require, exports) {
+    run(1);
+});
diff --git a/tests/baselines/reference/separateCompilationPlainFile-CommonJS.errors.txt b/tests/baselines/reference/separateCompilationPlainFile-CommonJS.errors.txt
new file mode 100644
index 0000000000000..d56e82fd6e181
--- /dev/null
+++ b/tests/baselines/reference/separateCompilationPlainFile-CommonJS.errors.txt
@@ -0,0 +1,10 @@
+tests/cases/compiler/separateCompilationPlainFile-CommonJS.ts(2,1): error TS1208: Cannot compile non-external modules when the '--separateCompilation' flag is provided.
+
+
+==== tests/cases/compiler/separateCompilationPlainFile-CommonJS.ts (1 errors) ====
+    
+    declare function run(a: number): void;
+    ~~~~~~~
+!!! error TS1208: Cannot compile non-external modules when the '--separateCompilation' flag is provided.
+    run(1);
+    
\ No newline at end of file
diff --git a/tests/baselines/reference/separateCompilationPlainFile-CommonJS.js b/tests/baselines/reference/separateCompilationPlainFile-CommonJS.js
new file mode 100644
index 0000000000000..cd82cdf20a6b2
--- /dev/null
+++ b/tests/baselines/reference/separateCompilationPlainFile-CommonJS.js
@@ -0,0 +1,8 @@
+//// [separateCompilationPlainFile-CommonJS.ts]
+
+declare function run(a: number): void;
+run(1);
+
+
+//// [separateCompilationPlainFile-CommonJS.js]
+run(1);
diff --git a/tests/baselines/reference/separateCompilationPlainFile-ES6.errors.txt b/tests/baselines/reference/separateCompilationPlainFile-ES6.errors.txt
new file mode 100644
index 0000000000000..6054ab552c8b9
--- /dev/null
+++ b/tests/baselines/reference/separateCompilationPlainFile-ES6.errors.txt
@@ -0,0 +1,10 @@
+tests/cases/compiler/separateCompilationPlainFile-ES6.ts(2,1): error TS1208: Cannot compile non-external modules when the '--separateCompilation' flag is provided.
+
+
+==== tests/cases/compiler/separateCompilationPlainFile-ES6.ts (1 errors) ====
+    
+    declare function run(a: number): void;
+    ~~~~~~~
+!!! error TS1208: Cannot compile non-external modules when the '--separateCompilation' flag is provided.
+    run(1);
+    
\ No newline at end of file
diff --git a/tests/baselines/reference/separateCompilationPlainFile-ES6.js b/tests/baselines/reference/separateCompilationPlainFile-ES6.js
new file mode 100644
index 0000000000000..1cb6082f1340d
--- /dev/null
+++ b/tests/baselines/reference/separateCompilationPlainFile-ES6.js
@@ -0,0 +1,8 @@
+//// [separateCompilationPlainFile-ES6.ts]
+
+declare function run(a: number): void;
+run(1);
+
+
+//// [separateCompilationPlainFile-ES6.js]
+run(1);
diff --git a/tests/baselines/reference/separateCompilationPlainFile-System.errors.txt b/tests/baselines/reference/separateCompilationPlainFile-System.errors.txt
new file mode 100644
index 0000000000000..716909cee4f36
--- /dev/null
+++ b/tests/baselines/reference/separateCompilationPlainFile-System.errors.txt
@@ -0,0 +1,10 @@
+tests/cases/compiler/separateCompilationPlainFile-System.ts(2,1): error TS1208: Cannot compile non-external modules when the '--separateCompilation' flag is provided.
+
+
+==== tests/cases/compiler/separateCompilationPlainFile-System.ts (1 errors) ====
+    
+    declare function run(a: number): void;
+    ~~~~~~~
+!!! error TS1208: Cannot compile non-external modules when the '--separateCompilation' flag is provided.
+    run(1);
+    
\ No newline at end of file
diff --git a/tests/baselines/reference/separateCompilationPlainFile-System.js b/tests/baselines/reference/separateCompilationPlainFile-System.js
new file mode 100644
index 0000000000000..c256ed7862a91
--- /dev/null
+++ b/tests/baselines/reference/separateCompilationPlainFile-System.js
@@ -0,0 +1,15 @@
+//// [separateCompilationPlainFile-System.ts]
+
+declare function run(a: number): void;
+run(1);
+
+
+//// [separateCompilationPlainFile-System.js]
+System.register([], function(exports_1) {
+    return {
+        setters:[],
+        execute: function() {
+            run(1);
+        }
+    }
+});
diff --git a/tests/baselines/reference/separateCompilationPlainFile-UMD.errors.txt b/tests/baselines/reference/separateCompilationPlainFile-UMD.errors.txt
new file mode 100644
index 0000000000000..c86daeabddfa7
--- /dev/null
+++ b/tests/baselines/reference/separateCompilationPlainFile-UMD.errors.txt
@@ -0,0 +1,10 @@
+tests/cases/compiler/separateCompilationPlainFile-UMD.ts(2,1): error TS1208: Cannot compile non-external modules when the '--separateCompilation' flag is provided.
+
+
+==== tests/cases/compiler/separateCompilationPlainFile-UMD.ts (1 errors) ====
+    
+    declare function run(a: number): void;
+    ~~~~~~~
+!!! error TS1208: Cannot compile non-external modules when the '--separateCompilation' flag is provided.
+    run(1);
+    
\ No newline at end of file
diff --git a/tests/baselines/reference/separateCompilationPlainFile-UMD.js b/tests/baselines/reference/separateCompilationPlainFile-UMD.js
new file mode 100644
index 0000000000000..6a145e7d239cb
--- /dev/null
+++ b/tests/baselines/reference/separateCompilationPlainFile-UMD.js
@@ -0,0 +1,17 @@
+//// [separateCompilationPlainFile-UMD.ts]
+
+declare function run(a: number): void;
+run(1);
+
+
+//// [separateCompilationPlainFile-UMD.js]
+(function (deps, factory) {
+    if (typeof module === 'object' && typeof module.exports === 'object') {
+        var v = factory(require, exports); if (v !== undefined) module.exports = v;
+    }
+    else if (typeof define === 'function' && define.amd) {
+        define(deps, factory);
+    }
+})(["require", "exports"], function (require, exports) {
+    run(1);
+});
diff --git a/tests/cases/compiler/separateCompilationPlainFile-AMD.ts b/tests/cases/compiler/separateCompilationPlainFile-AMD.ts
new file mode 100644
index 0000000000000..a1010ce3e8c86
--- /dev/null
+++ b/tests/cases/compiler/separateCompilationPlainFile-AMD.ts
@@ -0,0 +1,6 @@
+// @target: es5
+// @module: amd
+// @separateCompilation: true
+
+declare function run(a: number): void;
+run(1);
diff --git a/tests/cases/compiler/separateCompilationPlainFile-CommonJS.ts b/tests/cases/compiler/separateCompilationPlainFile-CommonJS.ts
new file mode 100644
index 0000000000000..532d97f09eb1c
--- /dev/null
+++ b/tests/cases/compiler/separateCompilationPlainFile-CommonJS.ts
@@ -0,0 +1,6 @@
+// @target: es5
+// @module: commonjs
+// @separateCompilation: true
+
+declare function run(a: number): void;
+run(1);
diff --git a/tests/cases/compiler/separateCompilationPlainFile-ES6.ts b/tests/cases/compiler/separateCompilationPlainFile-ES6.ts
new file mode 100644
index 0000000000000..20d4e8d79a285
--- /dev/null
+++ b/tests/cases/compiler/separateCompilationPlainFile-ES6.ts
@@ -0,0 +1,5 @@
+// @target: es6
+// @separateCompilation: true
+
+declare function run(a: number): void;
+run(1);
diff --git a/tests/cases/compiler/separateCompilationPlainFile-System.ts b/tests/cases/compiler/separateCompilationPlainFile-System.ts
new file mode 100644
index 0000000000000..6906571825438
--- /dev/null
+++ b/tests/cases/compiler/separateCompilationPlainFile-System.ts
@@ -0,0 +1,6 @@
+// @target: es5
+// @module: system
+// @separateCompilation: true
+
+declare function run(a: number): void;
+run(1);
diff --git a/tests/cases/compiler/separateCompilationPlainFile-UMD.ts b/tests/cases/compiler/separateCompilationPlainFile-UMD.ts
new file mode 100644
index 0000000000000..4ab45686c909c
--- /dev/null
+++ b/tests/cases/compiler/separateCompilationPlainFile-UMD.ts
@@ -0,0 +1,6 @@
+// @target: es5
+// @module: umd
+// @separateCompilation: true
+
+declare function run(a: number): void;
+run(1);