Flip Chip Ball Grid Array (FCBGA) packages, together with many other heterogeneous integration packages, are widely used in high I/O (Input/Output) density and high-performance computing applications. The thermal dissipation efficiency of such packages is often improved through the use of an external heat sink. However, the heat sink increases the solder joint inelastic strain energy density, and thus reduces the board-level thermal cycling test reliability. The present study constructs a three-dimensional (3D) numerical model to investigate the solder joint reliability of a lidless on-board FCBGA package with heat sink effects under thermal cycling testing, in accordance with JEDEC standard test condition G (a thermal range of −40 to 125 °C and a dwell/ramp time of 15/15 min). The validity of the numerical model is confirmed by comparing the predicted warpage of the FCBGA package with the experimental measurements obtained using a shadow moiré system. The effects of the heat sink and loading distance on the solder joint reliability performance are then examined. It is shown that the addition of the heat sink and a longer loading distance increase the solder ball creep strain energy density (CSED) and degrade the package reliability performance accordingly.