In a mixing bowl, whisk together soy sauce, brown sugar, pineapple juice, vegetable oil, rice vinegar, minced garlic, grated ginger, black pepper, salt, and red pepper flakes if using to create the marinade.
Place the chicken thighs in a resealable plastic bag or a shallow dish. Pour the marinade over the chicken, ensuring it's well-coated. Seal the bag or cover the dish and refrigerate for at least 1 hour, or up to overnight for maximum flavor.
Preheat your grill or grill pan over medium-high heat.
Remove the chicken from the marinade, letting any excess drip off. Discard the marinade.
Place the chicken on the preheated grill and cook for about 6-7 minutes on each side, or until the chicken reaches an internal temperature of 165°F (75°C).
Remove the chicken from the grill and let it rest for a few minutes before slicing.
Serve the Huli Huli Chicken garnished with sliced green onions and, if desired, grilled pineapple slices on the side.