Cut the chicken thighs into 1-inch pieces and set aside.
In a medium bowl, whisk together soy sauce, mirin, sake, brown sugar, ginger, garlic, and black pepper until the sugar dissolves.
Add the chicken pieces to the marinade, ensuring they are well coated. Cover and refrigerate for at least 30 minutes, or up to 2 hours for more flavor.
Preheat your grill to medium-high heat.
Thread the marinated chicken pieces onto the soaked wooden skewers, alternating with pieces of green onion if desired.
Place the skewers on the grill and cook for about 5-7 minutes on each side, or until the chicken is cooked through and has nice grill marks.
Brush with any remaining marinade during grilling for extra flavor.
Remove the skewers from the grill and let them rest for a few minutes before serving.
Serve hot, garnished with additional green onions if desired.