diff --git a/src/compiler/utilities.ts b/src/compiler/utilities.ts
index 31b464b81cea4..b4ef62c6c3e22 100644
--- a/src/compiler/utilities.ts
+++ b/src/compiler/utilities.ts
@@ -2330,7 +2330,9 @@ namespace ts {
 
     export function getSourceFilePathInNewDir(sourceFile: SourceFile, host: EmitHost, newDirPath: string) {
         let sourceFilePath = getNormalizedAbsolutePath(sourceFile.fileName, host.getCurrentDirectory());
-        sourceFilePath = sourceFilePath.replace(host.getCommonSourceDirectory(), "");
+        const commonSourceDirectory = host.getCommonSourceDirectory();
+        const isSourceFileInCommonSourceDirectory = host.getCanonicalFileName(sourceFilePath).indexOf(host.getCanonicalFileName(commonSourceDirectory)) === 0;
+        sourceFilePath = isSourceFileInCommonSourceDirectory ? sourceFilePath.substring(commonSourceDirectory.length) : sourceFilePath;
         return combinePaths(newDirPath, sourceFilePath);
     }