In a large bowl, whisk together the soy sauce, brown sugar, water, rice vinegar, garlic, ginger, black pepper, and red pepper flakes until the sugar is dissolved.
Add the chicken thighs to the marinade, ensuring they are well coated. Cover and refrigerate for at least 1 hour, or up to overnight for best flavor.
Preheat your oven to 375°F (190°C).
Place the marinated chicken thighs in a baking dish, pouring the marinade over the top.
Bake for 35-40 minutes, or until the chicken is cooked through and reaches an internal temperature of 165°F (74°C).
For extra caramelization, switch the oven to broil for the last 5 minutes of cooking, watching closely to prevent burning.
Remove from the oven and let the chicken rest for 5 minutes before serving. Garnish with sliced green onions and sesame seeds if desired.