In a medium bowl, whisk together the honey, soy sauce, minced garlic, grated ginger, sesame oil, rice vinegar, black pepper, and red pepper flakes (if using).
Place the chicken thighs in a large resealable plastic bag or a shallow dish, and pour the honey garlic marinade over the chicken. Seal the bag or cover the dish, ensuring the chicken is well-coated. Marinate in the refrigerator for at least 30 minutes, or up to 4 hours for more flavor.
Preheat your oven to 400°F (200°C). Remove the chicken from the marinade, reserving the marinade for later use.
Place the marinated chicken thighs in a baking dish and bake in the preheated oven for about 25-30 minutes, or until the internal temperature reaches 165°F (74°C).
While the chicken is baking, pour the reserved marinade into a small saucepan and bring it to a boil over medium heat. Reduce heat to low and let it simmer for about 5-10 minutes, or until slightly thickened.
Once the chicken is done, remove it from the oven and brush the thickened marinade on top of the chicken for extra flavor.
Let the chicken rest for a few minutes before slicing. Garnish with sliced green onions and sesame seeds before serving.
Notes
For extra flavor, marinate the chicken for up to 4 hours.