Purpose To evaluate the rate of peripapillary choroidal thinning in glaucoma patients and healthy controls using spectral domain optical coherence tomography. Design Cohort study. Methods Participants from the multicenter African Descent and Glaucoma Evaluation Study and Diagnostic Innovations in Glaucoma Study were included. The San Diego Automated Segmentation Algorithm was used to automatically segment and measure peripapillary choroidal thickness (PCT) from circle scans centered on the optic nerve head. The rate of PCT thinning was calculated using mixed effects models. Results Two hundred ninety-seven eyes with a median follow-up of 2.6 years were included. At baseline, the global mean PCT was significantly thinner in glaucoma patients than healthy control subjects (141.7 ± 66.3 μm vs 155.7 ± 64.8 μm, respectively; P <.001). However, when age was included in the model, this difference was no longer significant (P =.38). Both healthy controls and glaucoma patients had a significant decrease in mean (95% confidence interval) PCT change over time (−2.18 [−2.97 to −1.40 μm/year] and −1.88 [−3.08 to −0.67 μm/year], respectively) and mean PCT percent change over time (−3.32% [−4.36 to −2.27 μm/year] and −2.85% [−4.64 to −0.99 μm/year], respectively). No significant difference was found between healthy control subjects and glaucoma patients in the mean rate of PCT change (P =.28) or PCT percentage change over time (P =.23). Conclusions The rate of peripapillary choroidal thinning was not significantly different between healthy and glaucoma eyes during this relatively short follow-up period. Longer follow-up is needed to determine whether monitoring the rate of PCT change has a role in glaucoma management.