diff --git a/packages/babel-cli/src/babel/file.js b/packages/babel-cli/src/babel/file.js
index 7c38d3052f3d..d4ef573fb439 100644
--- a/packages/babel-cli/src/babel/file.js
+++ b/packages/babel-cli/src/babel/file.js
@@ -221,7 +221,10 @@ export default async function({
           },
         })
         .on("all", function(type: string, filename: string) {
-          if (!util.isCompilableExtension(filename, cliOptions.extensions)) {
+          if (
+            !util.isCompilableExtension(filename, cliOptions.extensions) &&
+            !filenames.includes(filename)
+          ) {
             return;
           }