diff --git a/compiler/clean.go b/compiler/clean.go
index 22b228e..90e9e94 100644
--- a/compiler/clean.go
+++ b/compiler/clean.go
@@ -35,6 +35,17 @@ func Clean(path string, opts *settings.Settings) {
 		helpers.CleanFile(scores[i].OutputPath)
 	}
 
+	// Remove empty category directories
+	if !opts.FlatOutputDir {
+		cat := scoreCategories(&scores)
+		for i := range cat {
+			dir := filepath.Join(opts.OutputDir, cat[i])
+			if t, err := helpers.EmptyDir(dir); t && err == nil {
+				helpers.CleanFile(dir)
+			}
+		}
+	}
+
 	// Remove LaTeX resources
 	texPath := filepath.Join(opts.OutputDir, opts.Name+".tex")
 	helpers.CleanFile(texPath)
diff --git a/helpers/file_utils.go b/helpers/file_utils.go
index 2c35881..04c5b9e 100644
--- a/helpers/file_utils.go
+++ b/helpers/file_utils.go
@@ -16,6 +16,7 @@ package helpers
 
 import (
 	"errors"
+	"io"
 	"os"
 	"path/filepath"
 	"time"
@@ -112,3 +113,17 @@ func CleanFile(path string) {
 		}
 	}
 }
+
+func EmptyDir(name string) (bool, error) {
+	f, err := os.Open(name)
+	if err != nil {
+		return false, err
+	}
+	defer f.Close()
+
+	_, err = f.Readdirnames(1) // Or f.Readdir(1)
+	if err == io.EOF {
+		return true, nil
+	}
+	return false, err // Either not empty or error, suits both cases
+}