diff --git a/lib/cli/watch-run.js b/lib/cli/watch-run.js
index 3d9eef6aeb..7b23d0fab2 100644
--- a/lib/cli/watch-run.js
+++ b/lib/cli/watch-run.js
@@ -145,15 +145,23 @@ class GlobFilesTracker {
   }
 
   regenerate() {
-    let watchIgnoreFlat = [];
+    const watchIgnoreSet = new Set();
     for (const pattern of this.watchIgnore) {
-      watchIgnoreFlat = watchIgnoreFlat.concat(glob.sync(pattern, { dot: true }));
+      glob.sync(pattern, { dot: true }).forEach(filePath => watchIgnoreSet.add(filePath));
     }
 
+    const globOpts = {
+      dot: true,
+      ignore: {
+        ignored: () => false,
+        childrenIgnored: pathToCheck => watchIgnoreSet.has(pathToCheck.relative())
+      }
+    };
+
     this.watchFilesSet.clear();
     for (const pattern of this.watchFiles) {
-      glob.sync(pattern, { dot: true }).forEach(pathToCheck => {
-        for (const watchIgnore of watchIgnoreFlat) {
+      glob.sync(pattern, globOpts).forEach(pathToCheck => {
+        for (const watchIgnore of watchIgnoreSet) {
           if (pathToCheck === watchIgnore) {
             return;
           }