Preheat your oven to 400°F (200°C).
In a large bowl, combine the grated ginger, minced garlic, soy sauce, honey, rice vinegar, sesame oil, black pepper, and red pepper flakes. Mix well to create a marinade.
Add the chicken thighs to the marinade, ensuring they are well coated. Let them marinate for at least 30 minutes at room temperature, or refrigerate for up to 2 hours for more flavor.
Place the marinated chicken thighs skin-side up on a baking sheet lined with parchment paper or in a baking dish.
Bake in the preheated oven for 35-40 minutes, or until the chicken is cooked through and the skin is crispy. The internal temperature should reach 165°F (75°C).
Remove from the oven and let rest for 5 minutes. Garnish with sliced green onions and sesame seeds before serving.