In a bowl, combine soy sauce, honey, rice vinegar, minced garlic, grated ginger, sesame oil, black pepper, and red pepper flakes if using. Whisk until the ingredients are well combined to create the marinade.
Place the chicken thighs in a resealable plastic bag or a shallow dish. Pour half of the marinade over the chicken, ensuring each thigh is well coated. Seal the bag or cover the dish and refrigerate for at least 1 hour, preferably overnight for deeper flavor.
Preheat your oven to 400°F (200°C).
Remove the chicken thighs from the marinade, allowing excess to drip off, and place them in a baking dish, skin-side up.
Use the remaining marinade to brush over the chicken thighs.
Bake in the preheated oven for 25-30 minutes, or until the chicken is cooked through (internal temperature of 165°F/75°C) and the skin is caramelized.
For an extra sticky glaze, switch the oven to broil for the last 2-3 minutes of cooking, watching carefully to prevent burning.
Once done, remove the chicken from the oven and let it rest for a few minutes before serving.
Garnish with sesame seeds and chopped green onions before plating.