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Step 1
Mix sesame seeds, chives, Aleppo-style pepper, and lemon zest in a small bowl to combine; season with salt.
Step 2
Combine brown sugar, mirin, soy sauce, and vinegar in a small saucepan. Transfer ¼ cup mixture to a large resealable plastic bag. Working one at a time, slice chicken thighs in half lengthwise. Add to bag with marinade and massage marinade into chicken. Chill at least 2 hours or up to 12 hours.
Step 3
Meanwhile, bring remaining marinade to a simmer over medium-high heat and cook until reduced by half and slightly thickened (just shy of syrupy), 8–10 minutes. Remove glaze from heat.
Step 4
Prepare a grill for medium-high, indirect heat (for a charcoal grill, bank coals on one side of grill; for a gas grill, leave one or two burners off). Oil grates. Thread chicken onto 6–8 skewers, folding and piling onto itself to form a compact shape. Season lightly with salt and grill over direct heat, turning every minute or so, until browned and beginning to char in spots, about 4 minutes. Move to cooler side of grill and continue to grill, basting lightly with glaze and turning every 30 seconds or so, until cooked through and coated with glaze, about 5 minutes longer. Serve chicken topped with sesame-citrus sprinkle.
Step 5
Do Ahead: Glaze can be made 12 hours ahead. Let cool; cover and chill. Bring to room temperature before using.