In a medium bowl, whisk together the soy sauce, honey, rice vinegar, minced garlic, grated ginger, sesame oil, and black pepper. This will be your marinade.
Place the chicken thighs in a large zip-top bag or shallow dish, then pour the marinade over the chicken. Seal the bag or cover the dish and marinate in the refrigerator for at least 30 minutes (or up to 4 hours for deeper flavor).
Preheat your oven to 400°F (200°C).
Line a baking dish with parchment paper for easy cleanup. Remove the chicken from the marinade, reserving the marinade for later.
Place the chicken thighs in the prepared baking dish and bake for 20 minutes.
Meanwhile, pour the reserved marinade into a small saucepan and bring to a boil over medium heat. Reduce the heat and let it simmer for about 5-7 minutes, or until it slightly thickens.
After 20 minutes of baking, remove the chicken from the oven and baste it with some of the thickened marinade. Return it to the oven for another 10-15 minutes, or until the chicken reaches an internal temperature of 165°F (75°C).
Once cooked, let the chicken rest for a few minutes before slicing. Drizzle any remaining thickened marinade over the sliced chicken.
Garnish with chopped green onions and sesame seeds before serving.