In a large bowl, whisk together honey, soy sauce, apple cider vinegar, olive oil, minced garlic, red pepper flakes, salt, and pepper until well combined.
Add the chicken thighs to the marinade, ensuring they are well coated. Cover and refrigerate for at least 30 minutes, or up to 2 hours for more flavor.
Preheat your oven to 400°F (200°C).
Line a baking sheet with parchment paper or lightly grease it. Place the marinated chicken thighs on the baking sheet, reserving the marinade.
Bake the chicken in the preheated oven for 25-30 minutes, or until the internal temperature reaches 165°F (75°C).
While the chicken is baking, pour the reserved marinade into a small saucepan. Bring it to a boil over medium heat and let it simmer for about 5-7 minutes, until it thickens slightly.
Once the chicken is done, remove it from the oven and brush it with the thickened marinade.
Garnish with chopped green onions and sesame seeds before serving.