Place the quail eggs in a small saucepan and add enough water to cover them by about 1 inch.
Bring the water to a boil over medium-high heat, then reduce to a simmer and cook the eggs for 3 minutes.
Turn off the heat, drain the hot water, and immediately transfer the eggs to a bowl of cold or ice water. Let cool for about 10 minutes.
Meanwhile, combine the soy sauce, 1/2 cup water, sugar, minced garlic, chopped green onion, and chopped chili (if using) in a 1.5 L mason jar or similar container and stir until the sugar dissolves.
Carefully peel the cooled quail eggs and place them in the jar with the marinade. Ensure the eggs are submerged in the liquid.
Cover the jar and refrigerate the eggs for at least overnight and up to 24 hours to develop flavor.
To serve, remove the eggs from the marinade and drizzle some of the marinade over them if desired.