To get ultrahigh stability of the dc high‐voltage (HV) output, we propose a novel compensation method for reducing the periodic ripple included in the output of a Cockcroft–Walton (CW) generator circuit. A compensating signal is injected into the circuit via the ground end to compensate various ripple harmonics at the HV end. Considering the nonlinearity of a CW circuit, we first compose the signal with the linear superposition of harmonics minimizing individual ripple spectral components, and then reduce the deviation due to the nonlinearity through the fine adjustment on the synthesized signal. An experiment testing the method has been carried out in an ultrahigh‐voltage electron microscope, compensating the ripple components from the fundamental to the ninth higher harmonics. Ripple has been decreased by above one order of magnitude, resulting in a percent ripple of less than 1×10−6.