In a small saucepan over medium heat, combine honey, red chili pepper flakes, and apple cider vinegar, and bring to a simmer. Stir and lower heat.
Continue to simmer at the lowest heat for 20 minutes to let the chili pepper flavor infuse. The honey will liquify, which is normal. If the honey is bubbling over then the heat is too high. Be sure the heat is as low as you can to maintain a simmer.
Remove from heat and place in a container (I like a glass mason jar). Will thicken up as it cools again. Optional: You can strain if desired but it is not necessary. Will last up to three months in a dark cupboard.