diff --git a/package.json b/package.json
index 264df28356d..b8d324bc683 100644
--- a/package.json
+++ b/package.json
@@ -56,7 +56,7 @@
   "bugs": "https://github.com/eslint/eslint/issues/",
   "dependencies": {
     "@eslint/eslintrc": "^1.3.3",
-    "@humanwhocodes/config-array": "^0.11.3",
+    "@humanwhocodes/config-array": "^0.11.5",
     "@humanwhocodes/module-importer": "^1.0.1",
     "@nodelib/fs.walk": "^1.2.8",
     "ajv": "^6.10.0",
diff --git a/tests/fixtures/ignores-subdirectory/eslint.config.js b/tests/fixtures/ignores-subdirectory/eslint.config.js
new file mode 100644
index 00000000000..2e1db61e7fe
--- /dev/null
+++ b/tests/fixtures/ignores-subdirectory/eslint.config.js
@@ -0,0 +1,3 @@
+module.exports = {
+    ignores: ["subdir"]
+};
diff --git a/tests/fixtures/ignores-subdirectory/subdir/subsubdir/a.js b/tests/fixtures/ignores-subdirectory/subdir/subsubdir/a.js
new file mode 100644
index 00000000000..e69de29bb2d
diff --git a/tests/lib/eslint/flat-eslint.js b/tests/lib/eslint/flat-eslint.js
index 150bdd584ad..ed08b36ff13 100644
--- a/tests/lib/eslint/flat-eslint.js
+++ b/tests/lib/eslint/flat-eslint.js
@@ -1102,7 +1102,7 @@ describe("FlatESLint", () => {
             });
 
             // https://github.com/eslint/eslint/issues/16354
-            it("should skip subdirectory files when ignore pattern matches subdirectory", async () => {
+            it("should skip subdirectory files when ignore pattern matches deep subdirectory", async () => {
                 eslint = new FlatESLint({
                     cwd: getFixturePath("ignores-directory")
                 });
@@ -1124,6 +1124,34 @@ describe("FlatESLint", () => {
 
             });
 
+            // https://github.com/eslint/eslint/issues/16414
+            it("should skip subdirectory files when ignore pattern matches subdirectory", async () => {
+                eslint = new FlatESLint({
+                    cwd: getFixturePath("ignores-subdirectory")
+                });
+
+                await assert.rejects(async () => {
+                    await eslint.lintFiles(["subdir/**/*.js"]);
+                }, /All files matched by 'subdir\/\*\*\/\*\.js' are ignored\./u);
+
+                const results = await eslint.lintFiles(["subdir/subsubdir/a.js"]);
+
+                assert.strictEqual(results.length, 1);
+                assert.strictEqual(results[0].filePath, getFixturePath("ignores-subdirectory/subdir/subsubdir/a.js"));
+                assert.strictEqual(results[0].warningCount, 1);
+                assert(results[0].messages[0].message.startsWith("File ignored"), "Should contain file ignored warning");
+
+                eslint = new FlatESLint({
+                    cwd: getFixturePath("ignores-subdirectory/subdir")
+                });
+
+                await assert.rejects(async () => {
+                    await eslint.lintFiles(["subsubdir/**/*.js"]);
+                }, /All files matched by 'subsubdir\/\*\*\/\*\.js' are ignored\./u);
+
+
+            });
+
             // https://github.com/eslint/eslint/issues/16340
             it("should lint files even when cwd directory name matches ignores pattern", async () => {
                 eslint = new FlatESLint({