Combine the vinegar, sugar, crushed red pepper flakes, seeds and dill with 1/2 cup water in a small saucepan. Bring to a boil, then remove from the heat.
Toss together the cucumber, jalapeño if using and onion, then transfer to a wide-mouth quart size Mason jar. Carefully pour over the warm vinegar mixture.
Cover and refrigerate for at least 12 hours or up to 7 days.