A magnetic resonance imaging apparatus according to an embodiment includes processing circuitry. The processing circuitry generates a plurality of cross-sectional images for setting a sectional position to be collected in main imaging based on a characteristic portion of a target detected in three-dimensional data. The processing circuitry lists the cross-sectional images on a display and superimposes a mark corresponding to the characteristic portion on at least one of the cross-sectional images. The processing circuitry receives a setting operation to determine the sectional position. The processing circuitry causes, when the mark is selected in the setting operation, a cross-sectional image to be emphasized a sectional position of which is defined using the characteristic portion corresponding to the mark among the listed cross-sectional images. The processing circuitry performs main imaging based on the sectional position after the setting operation.