We investigate the Higgs-Yukawa system with Majorana masses of a fermion within asymptotically safe quantum gravity. Using the functional renormalization group method we derive the beta functions of the Majorana masses and the Yukawa coupling constant and discuss the possibility of a non-trivial fixed point for the Yukawa coupling constant. In the gravitational sector we take into account higher derivative terms such as $R^2$ and $R_{mu u}R^{mu u}$ in addition to the Einstein-Hilbert term for our truncation. For a certain value of the gravitational coupling constants and the Majorana masses, the Yukawa coupling constant has a non-trivial fixed point value and becomes an irrelevant parameter being thus a prediction of the theory. We also discuss consequences due to the Majorana mass terms to the running of the quartic coupling constant in the scalar sector.