In a mixing bowl, whisk together 1.5 tbsp rice vinegar, 1/4 cup brown sugar, 1/2 cup low-sodium soy sauce, 3 tbsp gochujang, 1 tbsp grated ginger, and 4 minced garlic cloves to make the marinade.
Add the chicken thighs to the marinade and turn to coat all pieces evenly. Cover and refrigerate for at least 30 minutes or up to overnight.
When ready to cook, preheat the oven to 375°F (190°C) and line a baking sheet with foil.
Arrange the marinated chicken thighs on the prepared baking sheet, discarding any excess marinade from the bowl.
Bake the chicken for 20–25 minutes, until an internal temperature of 165°F (74°C) is reached and juices run clear.
While the chicken bakes, make the glaze by whisking together 1 tbsp rice vinegar, 1 tbsp low-sodium soy sauce, 1 tbsp gochujang, and 1/4 cup brown sugar in a small saucepan over medium heat; cook, whisking occasionally, about 5 minutes until slightly thickened without boiling.
In the last few minutes of baking, brush the chicken with the glaze. After removing the chicken from the oven, brush again with another coat of glaze before serving.