In a medium saucepan, combine apple cider vinegar, honey, red pepper flakes, salt, and black pepper. Heat over medium, stirring until honey dissolves, about 3-4 minutes.

Slice the red onions thinly, about ¼-inch thick, and place them in a clean glass jar.

Carefully pour the hot pickling mixture over the sliced onions, ensuring all slices are submerged.

Allow the jar to cool at room temperature for 15 minutes, then seal tightly and refrigerate.

Let the pickled onions marinate for at least 1 hour before serving for best flavor.