Preheat oven to 425 degrees F. Cut chicken breasts into 1/2" chunks. Place cut chicken, chopped onions, and 1 cup of BBQ sauce in 9"x9" baking dish. Mix well. Place in oven and bake for 30 to 40 minutes, until chicken is fully cooked.
While chicken is baking, spread the rest of the BBQ sauce over the crust evenly. Sprinkle half of the shredded pepperjack cheese over the BBQ sauce. Next, spread the green chiles evenly on the cheese. When the chicken is done baking, spread the chicken on top of the pizza crust. Top with the remaining cheese.
Turn oven temperature to 375 degrees F. Place the pizza on flat baking sheet and bake for 7 to 10 minutes. Bake until cheese is melted and crust is golden brown.