In a medium bowl, whisk together the honey, soy sauce, fresh lime juice, lime zest, minced garlic, and red pepper flakes until thoroughly combined.
Place the chicken thighs in a large resealable food-safe bag or covered container. Pour the honey lime chicken marinade over the chicken and turn the pieces several times to coat them evenly.
Refrigerate the chicken for at least 2 hours. For deeper flavor, marinate it overnight in the refrigerator.
Preheat the grill for direct cooking over high heat, approximately 450°F (232°C). Clean and lightly oil the grill grates if necessary.
Remove the chicken thighs from the marinade and discard the used marinade.
Arrange the chicken on the hot grill. Close the lid and grill for about 5–6 minutes, or until the chicken releases easily from the grates.
Turn the chicken and grill for another 4–5 minutes. Continue turning as needed until the outside is caramelized and the thickest part reaches a safe internal temperature of 165°F (74°C).
Transfer the Grilled Honey Lime Chicken to a clean platter. Rest for 5 minutes before slicing so the juices can redistribute, then serve warm.