Preheat the oven to 375°F (190°C).
In a mixing bowl, whisk together the pineapple juice, soy sauce, brown sugar, ketchup, rice vinegar, vegetable oil, minced garlic, grated ginger, black pepper, and red pepper flakes (if using) to create the marinade.
Place the chicken thighs in a baking dish and pour the marinade over the chicken, ensuring each piece is well-coated. Cover the dish with aluminum foil and let it marinate in the refrigerator for at least 30 minutes (or up to 4 hours for more flavor).
Remove the chicken from the refrigerator and discard the aluminum foil. Bake the chicken in the preheated oven for 30 minutes.
After 30 minutes, uncover the chicken and baste it with the marinade. Continue baking for an additional 10 minutes or until the chicken reaches an internal temperature of 165°F (74°C).
Once cooked, remove the chicken from the oven and let it rest for a few minutes. Garnish with sliced green onions and sesame seeds, if desired.
Serve the Baked Huli Huli Chicken with steamed rice and grilled vegetables for a complete meal.