Objective measurements of transverse chromatic aberration (TCA) between two or more wavelengths with an adaptive optics scanning laser ophthalmoscope (AOSLO) are very accurate, but frequent measurements are impractical in many experimental settings. Here, we demonstrate a pupil tracker that can accurately measure relative changes in TCA that are caused by small shifts in the pupil relative to the AOSLO imaging beam. Corrections for TCA caused by these shifts improve the measurement of TCA as a function of eccentricity, revealing a strong linear relationship. We propose that pupil tracking be integrated into AOSLO systems, where robust and unobtrusive control of TCA is required.