diff --git a/src/utils/general-utils.ts b/src/utils/general-utils.ts
index 89652cb..2456ffa 100755
--- a/src/utils/general-utils.ts
+++ b/src/utils/general-utils.ts
@@ -1,14 +1,30 @@
 import url from "url";
 import path from "path";
+import { realpathSync } from "fs";
 
 /* ****************************************************************************************************************** *
  * General Utilities & Helpers
  * ****************************************************************************************************************** */
 
 export const isURL = (s: string): boolean => !!s && (!!url.parse(s).host || !!url.parse(s).hostname);
+
 export const cast = <T>(v: any): T => v;
+
 export const isBaseDir = (baseDir: string, testDir: string): boolean => {
   const relative = path.relative(baseDir, testDir);
   return relative ? !relative.startsWith("..") && !path.isAbsolute(relative) : true;
 };
+
 export const maybeAddRelativeLocalPrefix = (p: string) => (p[0] === "." ? p : `./${p}`);
+
+export function tryRealpathNative(value: string) {
+  try {
+    return realpathSync.native(value);
+  } catch {
+    return value;
+  }
+}
+
+export function nativeRelativePath(from: string, to: string) {
+  return path.relative(tryRealpathNative(from), tryRealpathNative(to));
+}
diff --git a/src/utils/resolve-module-name.ts b/src/utils/resolve-module-name.ts
index b31158b..7abf35d 100755
--- a/src/utils/resolve-module-name.ts
+++ b/src/utils/resolve-module-name.ts
@@ -1,5 +1,5 @@
 import { VisitorContext } from "../types";
-import { isBaseDir, isURL, maybeAddRelativeLocalPrefix } from "./general-utils";
+import { isBaseDir, isURL, maybeAddRelativeLocalPrefix, nativeRelativePath } from "./general-utils";
 import * as path from "path";
 import { removeFileExtension, removeSuffix, ResolvedModuleFull, SourceFile } from "typescript";
 import { getOutputDirForSourceFile } from "./ts-helpers";
@@ -167,12 +167,12 @@ export function resolveModuleName(context: VisitorContext, moduleName: string):
 
     /* Remove base dirs to make relative to root */
     if (fileRootDir && moduleRootDir) {
-      srcFileOutputDir = path.relative(fileRootDir, srcFileOutputDir);
-      moduleFileOutputDir = path.relative(moduleRootDir, moduleFileOutputDir);
+      srcFileOutputDir = nativeRelativePath(fileRootDir, srcFileOutputDir);
+      moduleFileOutputDir = nativeRelativePath(moduleRootDir, moduleFileOutputDir);
     }
   }
 
-  const outputDir = path.relative(srcFileOutputDir, moduleFileOutputDir);
+  const outputDir = nativeRelativePath(srcFileOutputDir, moduleFileOutputDir);
 
   /* Compose final output path */
   const outputPath = maybeAddRelativeLocalPrefix(tsInstance.normalizePath(path.join(outputDir, outputBaseName)));