Use warm soapy water to wash a 1-pint jar, lid and sealing ring. Rinse well. Add the onions and chili flakes (if using to the jar), packing the onion jar as tightly as you can without smushing it. Make sure there is ½ to 1-inch of space from the rim of the jar to the tops of the onions.

Bring the vinegar, water, salt, and sugar to a boil in a small saucepan, whisking to dissolve the sugar and salt. Over the sink, pour the hot brine over the onions and submerge, pressing down on them with the end of a wooden spoon if needed.

Gently tap the jar against the counter a few times to remove all the air bubbles. Top off with more brine if necessary, and seal the jar(s).