To a small saucepan, add the rice wine vinegar, honey, crushed red pepper flakes, mustard seeds, dill and 1/2 cup of water. Bring to a boil, then remove from the heat.
Toss together the cucumber and red onion slices and transfer them to a wide-mouth quart-size mason jar. Carefully pour over the warm vinegar mixture. Cover and refrigerate for at least 12 hours and up to 7 days.