diff --git a/cli/source_maps.rs b/cli/source_maps.rs
index b3b8d7e56f..b2943cddb7 100644
--- a/cli/source_maps.rs
+++ b/cli/source_maps.rs
@@ -407,7 +407,7 @@ mod tests {
     assert_eq!(actual.message, "TypeError: baz");
     // Because this is accessing the live bundle, this test might be more fragile
     assert_eq!(actual.frames.len(), 1);
-    assert!(actual.frames[0].script_name.ends_with("js/window.ts"));
+    assert!(actual.frames[0].script_name.ends_with("/window.ts"));
   }
 
   #[test]
diff --git a/deno_typescript/compiler_main.js b/deno_typescript/compiler_main.js
index 0d51479d50..c83bbdec3c 100644
--- a/deno_typescript/compiler_main.js
+++ b/deno_typescript/compiler_main.js
@@ -109,6 +109,13 @@ const ops = {
   setEmitResult: 53
 };
 
+/**
+ * @type {Map<string, string>}
+ */
+const moduleMap = new Map();
+
+const externalSpecifierRegEx = /^file:\/{3}\S+\/js(\/\S+\.ts)$/;
+
 /**
  * This is a minimal implementation of a compiler host to be able to allow the
  * creation of runtime bundles.  Some of the methods are implemented in a way
@@ -176,18 +183,34 @@ class Host {
         .replace("/index.d.ts", "");
     }
 
+    // This looks up any modules that have been mapped to internal names
+    if (moduleMap.has(fileName)) {
+      fileName = moduleMap.get(fileName);
+    }
+
     const { sourceCode, moduleName } = dispatch("readFile", {
       fileName,
       languageVersion,
       shouldCreateNewSourceFile
     });
 
+    // If we match the external specifier regex, we will then create an internal
+    // specifier and then use that when creating the source file
+    let internalModuleName = moduleName;
+    const result = externalSpecifierRegEx.exec(moduleName);
+    if (result) {
+      const [, specifier] = result;
+      const internalSpecifier = `$deno$${specifier}`;
+      moduleMap.set(internalSpecifier, moduleName);
+      internalModuleName = internalSpecifier;
+    }
+
     const sourceFile = ts.createSourceFile(
-      fileName,
+      internalModuleName,
       sourceCode,
       languageVersion
     );
-    sourceFile.moduleName = moduleName;
+    sourceFile.moduleName = internalModuleName;
     return sourceFile;
   }
 
@@ -247,11 +270,17 @@ class Host {
    * @return {Array<ts.ResolvedModule | undefined>}
    */
   resolveModuleNames(moduleNames, containingFile) {
+    // If the containing file is an internal specifier, map it back to the
+    // external specifier
+    containingFile = moduleMap.has(containingFile)
+      ? moduleMap.get(containingFile)
+      : containingFile;
     /** @type {string[]} */
     const resolvedNames = dispatch("resolveModuleNames", {
       moduleNames,
       containingFile
     });
+    /** @type {ts.ResolvedModule[]} */
     const r = resolvedNames.map(resolvedFileName => {
       const extension = getExtension(resolvedFileName);
       return { resolvedFileName, extension };