In a medium saucepan, combine apple cider vinegar, honey, red pepper flakes, salt, and black pepper. Heat over medium heat for about 5 minutes, stirring gently until the honey completely dissolves.

Thinly slice red onion to about a quarter-inch thickness. Chill the onion in the refrigerator for a few minutes before slicing to minimize tears.

Place the sliced onions in a clean, heat-safe jar or bowl and pour the hot vinegar mixture over the onions, ensuring they are fully submerged.

Let the combined ingredients cool to room temperature for about 15 minutes, then refrigerate for at least an hour for optimal flavor infusion.