In a large bowl, combine the soy sauce, honey, rice vinegar, red pepper flakes, and black pepper. Mix well to create the marinade.
Add the chicken thighs to the marinade, ensuring they are well coated. Cover and refrigerate for at least 30 minutes, or up to 2 hours for more flavor.
Heat the vegetable oil in a large skillet over medium-high heat. Add the chopped onion and sauté for about 3-4 minutes until softened.
Add the minced garlic and grated ginger to the skillet, cooking for an additional 1-2 minutes until fragrant.
Remove the chicken from the marinade (reserving the marinade) and add it to the skillet. Cook for about 6-8 minutes on each side, or until the chicken is cooked through and has a nice golden brown color.
Pour the reserved marinade into the skillet and bring to a simmer. Cook for an additional 2-3 minutes, allowing the sauce to thicken slightly.
Remove from heat and garnish with chopped green onions and sesame seeds, if using. Serve hot over rice or with steamed vegetables.