Optical coherence tomography (OCT) systems utilize 2D scanning methods to acquire reflectance-based volumetric images of samples, such as the human retina, with micrometer-scale depth resolution. A common method for performing this scanning at high speeds is to use a pair of sequential, single-axis galvanometer scanners. An undesired effect of using separated scanners is the variation in the beam position at the pupil plane, a phenomenon known as beam wander or pupil wobble. This can lead to loss of signal and vignetting artifacts in the resulting images. To overcome these limitations, we propose a method to deterministically analyze the pupil wobble in a given retinal OCT system and to correct for the displacement using pupil tracking OCT with a 2D scanning mirror placed anti-conjugate to the pupil plane. We demonstrate that we can model the pattern of pupil wobble present in any OCT system both theoretically and empirically and then use a pupil tracking system to correct for the displacement of the beam to acquire OCT images without the imposed artifacts.