Preheat your oven to 375°F (190°C).
In a mixing bowl, whisk together the pineapple juice, soy sauce, brown sugar, apple cider vinegar, minced garlic, grated ginger, black pepper, and red pepper flakes until well combined.
Place the chicken thighs in a baking dish and pour the marinade over them, making sure they are well coated. Allow the chicken to marinate for at least 30 minutes.
Cover the dish with aluminum foil and place it in the preheated oven.
Bake the chicken for 30 minutes covered, then remove the foil and bake for an additional 15 minutes or until the chicken is cooked through.
For extra caramelization, you can broil the chicken for 2-3 minutes at the end, watching closely to prevent burning.
Once done, remove from the oven and let it rest for a few minutes.
Garnish with chopped green onions before serving.