A magnetic resonance imaging apparatus has a controller which controls an operation of a scan section in such a manner that the scan section executes a scan in an imaging sequence, based on the imaging sequence condition set so as to correspond to a slice tracking method by an imaging sequence condition setting unit, and controls the operation of at least one of the scan section and an image reconstruction unit, based on a phase difference calculated by a phase difference calculation unit so as to eliminate the phase difference at which phases of the magnetic resonance signals produced in an imaging slice areas change, when an RF pulse subsequent to having been adjusted in frequency so as to the slice tracking method is transmitted upon execution of the scan in the imaging sequence.