Heat the oven to 400°F and lightly oil a baking dish just large enough to hold the thighs in one layer. Pat chicken dry and season with salt and pepper.
Arrange thighs unfolded in the dish and bake for 12 minutes. Whisk honey, soy sauce, vinegar, garlic, ginger and water in a small bowl.
Brush half the glaze over the chicken and bake for 8 minutes. Brush with the remaining glaze and return to the oven.
Bake for 5 to 10 minutes more until browned in places and the thickest part of every thigh reaches at least 165°F.
Rest for 5 minutes, then spoon a little hot pan sauce over each thigh and serve.