The observation of blood oxygenation level-dependent (BOLD) effect in functional magnetic resonance imaging (fMRI) studies is often hampered by the presence of magnetic field inhomogeneities. These are caused by abrupt changes in the magnetic susceptibility that typically occur near air/tissue interfaces and may result in substantial image distortions and signal losses. In this article, we investigate the effect of susceptibility-induced magnetic field inhomogeneities on the signal intensity (I) and the BOLD sensitivity (BS) for two different phase encoding schemes in blipped echo-planar imaging (EPI), which use either positive (EPIpos) or negative (EPIneg) phase gradient blips for stepping through k-space. Based on magnetic field maps, we generate computer simulations of I and BS for both phase encoding schemes and demonstrate good agreement with the experimental image intensities. We show that regions compromised by susceptibility effects are affected very differently by EPIpos and EPIneg. Further simulations are performed in two representative regions of interest (orbitofrontal cortex and lower temporal lobe) to investigate the dependence of I and BS on the slice angle (alpha), the magnitude of a moderate compensation gradient applied in the slice direction (GScomp), and the phase encoding scheme. We find that I and BS can be considerably increased if the appropriate phase encoding scheme is applied in addition to optimizing alpha and GScomp. Our results suggest that this optimization method would be useful in future fMRI studies to improve the sensitivity in regions compromised by susceptibility effects.