In a bowl, whisk together soy sauce, honey, brown sugar, Dijon mustard, garlic, smoked paprika, black pepper, salt, olive oil, vinegar, and chili flakes. Place the chicken thighs in a resealable bag or shallow dish, then pour the marinade over them. Cover and refrigerate for at least 1 hour (or overnight for deeper flavor).
Preheat the grill to medium heat (about 375ยฐF). Lightly oil the grates to prevent sticking. Remove the chicken from the marinade and let excess drip off. Place the thighs on the grill and cook for 6-7 minutes per side, brushing with extra marinade occasionally, until the internal temperature reaches 165ยฐF.
In the final few minutes, increase the heat slightly to caramelize the glaze. Be careful not to burn the sugars. Once done, transfer the chicken to a plate and let it rest for 5 minutes to retain juiciness.
Slice or serve whole with your favorite sides like grilled vegetables, rice, or a fresh salad. Drizzle any extra juices over the top for added flavor.