Geopotential and orthometric height differences between distant points can be measured via timescale comparisons between atomic clocks. Modern optical atomic clocks achieve statistical uncertainties on the order of 10−18, allowing height differences of around 1 cm to be measured. Frequency transfer via free-space optical links will be needed for measurements where linking the clocks via optical fiber is not possible, but requires line of sight between the clock locations, which is not always practical due to local terrain or over long distances. We present an active optical terminal, phase stabilization system, and phase compensation processing method robust enough to enable optical frequency transfer via a flying drone, greatly increasing the flexibility of free-space optical clock comparisons. We demonstrate a statistical uncertainty of 2.5×10−18 after 3 s of integration, corresponding to a height difference of 2.3 cm, suitable for applications in geodesy, geology, and fundamental physics experiments.