Pupil stability is one of the factors which limit the performance and operational stability of adaptive optics (AO) systems. This paper analyses two pupil-tracking methods to measure the lateral pupil shift: the first one utilizes the fluxes in all outer edge sub-apertures of a Shack-Hartmann sensor and the second one utilizes the real-time interaction matrix used in an AO system. Experiments with 9×9 Shack-Hartmann sensor are conducted to verify both pupil-tracking algorithms. The results show that both algorithms are effective, after two correction steps, the residual pupil shift is reduced to less than 5% of a Shack-Hartmann sub-aperture.