In a large bowl, combine the soy sauce, honey, rice vinegar, grated ginger, red pepper flakes, and black pepper. Whisk until well blended.
Add the chicken thighs to the marinade, ensuring they are fully 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 sliced onion and sauté for about 3-4 minutes until softened.
Remove the chicken from the marinade (reserving the marinade) and add it to the skillet. Cook for 5-7 minutes on each side until the chicken is browned and cooked through.
Pour the reserved marinade into the skillet and bring to a simmer. Cook for an additional 3-4 minutes, allowing the sauce to thicken slightly.
Remove from heat and garnish with sliced green onions and sesame seeds before serving.