diff --git a/ktlint-cli/src/main/kotlin/com/pinterest/ktlint/cli/internal/FileUtils.kt b/ktlint-cli/src/main/kotlin/com/pinterest/ktlint/cli/internal/FileUtils.kt
index a371331fbb..a480371f74 100644
--- a/ktlint-cli/src/main/kotlin/com/pinterest/ktlint/cli/internal/FileUtils.kt
+++ b/ktlint-cli/src/main/kotlin/com/pinterest/ktlint/cli/internal/FileUtils.kt
@@ -137,8 +137,13 @@ internal fun FileSystem.fileSequence(
                         dirAttr: BasicFileAttributes,
                     ): FileVisitResult =
                         if (Files.isHidden(dirPath)) {
-                            LOGGER.trace { "- Dir: $dirPath: Ignore" }
-                            FileVisitResult.SKIP_SUBTREE
+                            if (dirPath == commonRootDir) {
+                                LOGGER.trace { "- Dir: $dirPath: Traverse started from hidden directory" }
+                                FileVisitResult.CONTINUE
+                            } else {
+                                LOGGER.trace { "- Dir: $dirPath: Ignore traversal of hidden directory" }
+                                FileVisitResult.SKIP_SUBTREE
+                            }
                         } else {
                             LOGGER.trace { "- Dir: $dirPath: Traverse" }
                             FileVisitResult.CONTINUE
diff --git a/ktlint-cli/src/test/kotlin/com/pinterest/ktlint/cli/internal/FileUtilsTest.kt b/ktlint-cli/src/test/kotlin/com/pinterest/ktlint/cli/internal/FileUtilsTest.kt
index bb108da1d9..3f9c993ad8 100644
--- a/ktlint-cli/src/test/kotlin/com/pinterest/ktlint/cli/internal/FileUtilsTest.kt
+++ b/ktlint-cli/src/test/kotlin/com/pinterest/ktlint/cli/internal/FileUtilsTest.kt
@@ -26,9 +26,9 @@ internal class FileUtilsTest {
     private val javaFileRootDirectory = "Root.java"
     private val ktFileRootDirectory = "Root.kt"
     private val ktsFileRootDirectory = "Root.kts"
-    private val javaFileInHiddenDirectory = "project1/.git/Ignored.java"
-    private val ktFileInHiddenDirectory = "project1/.git/Ignored.kt"
-    private val ktsFileInHiddenDirectory = "project1/.git/Ignored.kts"
+    private val javaFileInHiddenDirectory = "project1/.hidden/Ignored.java"
+    private val ktFileInHiddenDirectory = "project1/.hidden/Ignored.kt"
+    private val ktsFileInHiddenDirectory = "project1/.hidden/Ignored.kts"
     private val javaFileInProjectRootDirectory = "project1/ProjectRoot.java"
     private val ktFileInProjectRootDirectory = "project1/ProjectRoot.kt"
     private val ktsFileInProjectRootDirectory = "project1/ProjectRoot.kts"
@@ -106,6 +106,17 @@ internal class FileUtilsTest {
             )
     }
 
+    @Test
+    fun `Given the root directory where scanning starts is hidden, then the patterns should work`() {
+        val foundFiles =
+            getFiles(
+                patterns = listOf("*.kt"),
+                rootDir = ktlintTestFileSystem.resolve("project1/.hidden"),
+            )
+
+        assertThat(foundFiles).containsExactlyInAnyOrder(ktFileInHiddenDirectory)
+    }
+
     @Test
     fun `Given some patterns including a negate pattern and no workdir then select all files except files in the negate pattern`() {
         val foundFiles =