Preheat oven to 350 degrees. Coat a baking pan with cooking spray.
Place onions in a small microwave-safe bowl. Cook in the microwave for about 1 minute to soften. Mix onions into pizza sauce.
Place chicken breasts in pan. Top each breast with ⅓ cup pizza sauce. Place 2 slices of chopped pepperoni slices on top of each chicken breast. Sprinkle each with ¼ cup cheese.
Place pan in the oven and bake for about 25-30 minutes until chicken is cooked through.