Preheat your oven to 400°F (200°C). Line a baking dish with aluminum foil for easier cleanup.
In a medium bowl, whisk together the soy sauce, honey, brown sugar, rice vinegar, sesame oil, garlic, ginger, black pepper, and red pepper flakes until well combined.
Place the chicken thighs in the prepared baking dish, skin side up. Pour the marinade over the chicken, ensuring each piece is well coated.
Bake in the preheated oven for 35-40 minutes, basting the chicken with the sauce halfway through cooking. The chicken should be cooked through and have a nice glaze.
For extra crispiness, switch the oven to broil and broil the chicken for an additional 2-3 minutes, watching closely to prevent burning.
Remove from the oven and let the chicken rest for 5 minutes. Garnish with sliced green onions and sesame seeds before serving.