The visco-plastic behaviour of solder joints of two models of a flip chip FC48D6.3C457DC mounted on a printed circuit board (PCB) via SnAgCu solder is investigated using Anand's model. While the bumps of one of the models are realistic with 6 μm thickness of intermetallic compound (IMC) at interconnects of solder and bond pads, the other are made up of conventional bumps without IMC at these interconnects. The solder bump profiles were created using a combination of analytical method and construction geometry. The assembled package on PCB was accelerated thermally cycled (ATC) using IEC standard 60749-25. It was found in the result of the simulation that IMC does not only impact solder joint reliability but also is a key factor of fatigue failure of solder joints. The IMC sandwiched between bond pad at chip side and solder bulk is the most critical and its interface with solder bulk is the most vulnerable site of damage. With reference to our results, it is proposed that non inclusion of IMC in solder joint models composed of Sn-based solder and metalized copper substrate is one of the major causes of the discrepancy on solder joint fatigue life predicted using finite element modelling and the one obtained through experimental investigation.