Whisk together orange juice, brown sugar, rice vinegar, fish sauce, soy sauce, ginger, and red pepper flakes in a large bowl.
Mix in chicken pieces and toss to evenly coat. Cover the bowl with plastic wrap and marinate in the refrigerator for 1 hour.
Drain chicken thoroughly in a colander, reserving marinade.
Heat a large nonstick skillet over high heat. Cook and stir chicken in the hot skillet for 2 minutes; spoon out any excess liquid. Continue to cook and stir until chicken caramelizes, 6 to 7 minutes.
Stir in white portions of green onions, garlic, and orange zest; cook and stir for 2 to 3 minutes. Pour in ½ of the reserved marinade; discard remaining marinade. Simmer until reduced and thickened, 3 to 4 minutes.
Stir in bell pepper, sugar snap peas, and jalapeño pepper; cook and stir until vegetables are warmed, about 2 minutes. Stir in green portions of green onions; cook and stir 1 minute.
Remove from heat. Garnish with cilantro and serve.
