According to one embodiment, an MRI apparatus includes a gradient coil, an RF coil, an RF receiver, and processing circuitry which controls these components to perform each pulse sequence. The processing circuitry sets a main-scan pulse sequence, a first pulse sequence which includes application of a gradient magnetic field in a readout direction, and a second pulse sequence which includes application of the gradient magnetic field in a readout direction, and whose acquisition region is shifted from the first pulse sequence. The processing circuitry reconstructs image data of the main scan, based on magnetic resonance signals acquired by the main-scan pulse sequence and phase difference data in the readout direction between first k-space data generated from the magnetic resonance signals acquired by the first pulse sequence and second k-space data generated from the magnetic resonance signals acquired by the second pulse sequence.