Ultrathin CoFeB/MgO/CoFeB system with perpendicular magnetic anisotropy is a promising candidate for the high density magnetic random access memory. However, a dipolar interaction between the CoFeB layers may introduce a minor loop shift (Hs) and causes uncertainty during the operation. In this report, we systematically studied the dipolar effect in these structures and found that the coupling may be either ferromagnetic or antiferromagnetic (15 Oe > Hs > −15 Oe) depending upon the CoFeB thickness (0.9–1.4 nm). A modified Fabry-Perot model, which accounts the Bloch wave interference, may explain the present observations of the dipolar effect in the perpendicular junctions of CoFeB/MgO/CoFeB.