Provided is a magnetic resonance imaging (MRI) apparatus for generating an MR image based on a steady state free procession (SSFP) sequence. The MRI apparatus includes: a radio frequency (RF) controller configured to apply to an object a first RF pulse corresponding to a first slice and a second RF pulse corresponding to a second slice; a gradient magnetic field controller configured to control respective gradient magnetic fields in a first direction corresponding to the first and second RF pulses, from among spatial encoding gradients, to have opposite polarities with respect to each other; a data acquisition unit configured to acquire first and second MR signals corresponding to the first and second slices; and an image processor configured to generate first and second MR images corresponding to the first and second slices, respectively, based on the acquired first and second MR signals.