Electron paramagnetic resonance (EPR) powered by a free electron laser (FEL) has been shown to dramatically expand the capabilities of EPR at frequencies above ~100 GHz, where other high-power sources are unavailable. High-power pulses are necessary to achieve fast (<10 ns) spin rotations in order to alleviate the limited excitation bandwidth and time resolution that typically hamper pulsed EPR at these high frequencies. While at these frequencies, an FEL is the only source that provides ~1 kW of power and can be tuned continuously up to frequencies above 1 THz, it has only recently been implemented for one- and two-pulse EPR, and the capabilities of the FEL as an EPR source are still being expanded. This manuscript presents phase cycling of two pulses in an FEL-EPR spectrometer operating at 240 GHz. Given that the FEL, unlike amplifiers, cannot be easily phase-locked to a reference source, we instead apply retrospective data processing to measure the relative phase of each FEL pulse in order to correct the signal phase accordingly. This allows the measured signal to be averaged coherently, and the randomly changing phase of the FEL pulse results in a stochastic phase cycle, which, in the limit of many pulses, efficiently cancels artifacts and improves sensitivity. Further, the relative phase between the first and second pulse, which originates from the difference in path length traversed by each pulse, can be experimentally measured without phase-sensitive detection. We show that the relative phase of the two pulses can be precisely tuned, as well as distinctly switched by a fixed amount, with the insertion of a dielectric material into the quasi-optical path of one of the pulses. Taken together, these techniques offer many of the advantages of arbitrary phase control, and allow application of phase cycling to dramatically enhance signal quality in pulsed EPR experiments utilizing high-power sources that cannot be phase-locked.