A method of manufacture of an integrated circuit packaging system includes: providing a semiconductor wafer having a chip pad; attaching a wafer frame to the semiconductor wafer, the wafer frame having a horizontal cover integral to a protruding connector with the protruding connector on the chip pad; forming an underfill around the protruding connector and between the horizontal cover and the semiconductor wafer; removing the horizontal cover exposing the underfill and the protruding connector; and singulating an integrated circuit package from the semiconductor wafer.