Eye tracking is a useful tool when studying the oscillatory eye movements associated with nystagmus. However, this oscillatory nature of nystagmus is problematic during calibration since it introduces uncertainty about where the person is actually looking. This renders comparisons between separate recordings unreliable. Still, the influence of the calibration protocol on eye movement data from people with nystagmus has not been thoroughly investigated. In this work, we propose a calibration method using Procrustes analysis in combination with an outlier correction algorithm, which is based on a model of the calibration data and on the geometry of the experimental setup. The proposed method is compared to previously used calibration polynomials in terms of accuracy, calibration plane distortion and waveform robustness. Six recordings of calibration data, validation data and optokinetic nystagmus data from people with nystagmus and seven recordings from a control group were included in the study. Fixation errors during the recording of calibration data from the healthy participants were introduced, simulating fixation errors caused by the oscillatory movements found in nystagmus data. The outlier correction algorithm improved the accuracy for all tested calibration methods. The accuracy and calibration plane distortion performance of the Procrustes analysis calibration method were similar to the top performing mapping functions for the simulated fixation errors. The performance in terms of waveform robustness was superior for the Procrustes analysis calibration compared to the other calibration methods. The overall performance of the Procrustes calibration methods was best for the datasets containing errors during the calibration.