In a large bowl, whisk together soy sauce, brown sugar, ketchup, rice vinegar, sesame oil, garlic, ginger, black pepper, and red pepper flakes (if using) until well combined.
Add chicken thighs to the marinade, ensuring they are fully coated. Cover and refrigerate for at least 2 hours, or overnight for best flavor.
Preheat your grill to medium-high heat. Remove chicken from the marinade, reserving the marinade for basting.
Grill the chicken for about 6-7 minutes per side, basting with the reserved marinade during the last few minutes of cooking. Cook until the internal temperature reaches 165°F.
Remove chicken from the grill and let it rest for 5 minutes before serving.
Garnish with sliced green onions and sesame seeds before serving.