In a large bowl, whisk together soy sauce, white and light green parts of green onions, sliced onion, sugar, garlic, sesame seeds, sesame oil, red pepper flakes, ginger, and black pepper.
Add the thinly sliced beef and toss until evenly coated.
Cover and refrigerate for at least 1 hour (or up to 24 hours for deeper flavor).
Heat a large skillet or wok over medium-high heat.
Cook the beef in batches, along with the marinade, for about 4–5 minutes until fully cooked.
Add honey during cooking to help caramelize the meat.
Garnish with the dark green parts of the green onions before serving.