In a medium saucepan, bring the vinegar, sugar, salt, red pepper flakes, mustard seeds, garlic, and pepper to a boil. Set aside for 30 minutes to cool.
Pour the liquid into a large Ziploc bag or plastic container. Add the cucumber, onion slices, and fresh dill. Shake and/or massage to mix. Let the mixture sit in the refrigerator for 15 to 20 minutes (or longer) before serving.