A system and method for medical imaging using a magnetic resonance imaging system includes performing a segmented echo planar imaging (EPI) pulse sequence. The pulse sequence includes performing multiple radio frequency (RF) excitation pulses designed to excite multiple imaging slices across the subject simultaneously. A gradient encoding scheme applied along the slice-encoding direction is implemented to impart controlled phase shifts to the different imaging slices. Additionally, the multiple RF excitation pulses can be designed to further control an overlap of imaging data acquired from adjacent slices of the multiple imaging slices based on a selected offset. The acquired imaging data is reconstructed using a parallel imaging reconstruction method that separates overlapped slices in the imaging data to provide a series of images with respective images for each of the multiple imaging slices across the subject.