Many cellular activities involving cell membrane manifest through changes in membrane capacitance. The accuracy and precision of cell membrane capacitance measurement is limited by the measuring system, which distorts membrane current responses used for analysis of impedance parameters. We developed a practical deconvolution procedure for reconstruction of the time course of membrane current and applied it to current responses recorded at step voltage changes by the whole-cell patch-clamp technique. In contrast to the recorded current responses, the reconstructed current responses could be exactly described by adequate impedance models of the recorded circuit. Deconvolution of membrane currents improved the performance of the square-wave method of high-resolution membrane capacitance recording by providing higher accuracy in a wider range of cell sizes and by eliminating cross-talk errors in parameter estimates. This allowed resolving instabilities in the recording conditions arising from parasitic capacitance and seal resistance variation. Complex tests on hardware models, on simulated data sets, and on living cells confirmed reliability of the deconvolution method for membrane capacitance recording. The aptitude of the method was demonstrated in isolated cardiac myocytes by recording spontaneous vesicular events, by discerning formation of a fusion pore, and by revealing artefacts due to unstable seal resistance.