Rinse the chicken thighs under cold water, pat dry, and trim excess fat.
In a medium bowl, combine soy sauce, honey, apple cider vinegar, ketchup, minced garlic, ground ginger, black pepper, and red pepper flakes. Whisk until smooth.
Place chicken thighs in a bowl or resealable bag, pour marinade over, and coat well. Marinate for at least 30 minutes, preferably up to 4 hours.
Preheat oven to 400°F. Line a baking dish with foil and place a wire rack inside. Arrange chicken thighs skin-side up on the rack and bake for 35-40 minutes until internal temperature reaches 165°F.
While chicken bakes, bring reserved marinade to a boil in a saucepan and simmer for 5 minutes until thickened. Brush over chicken before serving and garnish with sesame seeds and green onions.