In this paper, the effect of magnetic field on the wave propagation in rectangular nanoplates based on two-variable refined plate theory is studied. In order to capture the size effects, the strain gradient theory with one length scale parameter is used. From our knowledge, it is the first time that two-variable refined plate theory is adopted for studying bulk waves in nanoplates. This type of refined plate theory has only two unknowns which reduces the complexity of the governing equations. To show the accuracy of this work, several comparisons are made with available results in open literature.