Beat flour, 1 cup brown sugar and 1/2 cup butter until well blended (mixture will be dry and crumbly). Firmly press into prepared pan. Sprinkle pecans over flour mixture.
In a small saucepan, combine remaining brown sugar and remaining butter. Bring to a boil over medium heat. Boil until sugar is dissolved, stirring constantly, about 1 minute. Carefully pour mixture over pecans. Bake until bubbly and edges start to brown, 15-20 minutes.
Remove from oven. Immediately sprinkle with chocolate chips. Let stand until chocolate begins to melt; spread evenly. Cool completely in pan on a wire rack. Lifting with parchment, remove from pan. Cut into squares.