Electromigration in the Cu/In/Cu flip chip joint system was investigated at a temperature of 398 K with a current density of 20 kA/cm2. Indium was transported towards the anode, and a large void nucleated by electromigration at the In/Cu11In9 interface in the highest current density region near the cathode. It was found that a unique solder bump deformation towards the cathode occurred in the early stage of the electromigration test, when no underfill material was used. When the underfill material was used to fill the space between the chip and the substrate, the electromigration lifetime in the joint was prolonged by more than ten folds in comparison with that of the joint without underfill. This was a result from that indium transport was inhibited due to a larger backstress induced by the constraint of the underfill.