We theoretically study specific non-stationary dynamics of gyrotrons generation in conditions of significant excess of the operating current over the starting value. In this case, gyrotrons with continuous electron beams unpredictably emit “giant” ultrashort radiation spikes, which can be interpreted as microwave rogue waves. Within the frame of the average approach and direct 3D particle-in-cell simulations, we demonstrate that the occurrence of gyrotron rogue waves can be regularized by periodic injection of an electron beam. More regular formation of rogue waves would enhance interest in the implementation of such systems for possible applications.