A Monte Carlo method that calculates the transient behavior of neutron flux in the frequency domain is proposed in this study. A time-dependent neutron transport equation, in which the neutron source term varies over time while other properties remain constant, is Fourier transformed to obtain the transport equation in the frequency domain. The complex-valued transport equation in the frequency domain is subsequently solved with the complex-valued weight Monte Carlo method for each frequency contained in the Fourier transformed source intensity. The effect of delayed neutrons can be easily included in this frequency domain transport equation. Using the inverse Fourier transformation of the neutron flux in the frequency domain, we can obtain the time variation of the flux. This method is applicable to transient analyses of a subcritical system with a time-varying neutron source intensity. Several numerical examples indicate that the newly developed frequency domain calculation method provides good results compared to the time-dependent calculation method in the time domain. The computation time in the frequency domain is significantly shorter than that in the time domain, particularly for a nearly critical system.