In myopia research, changes of choroidal thickness in response to optically induced signals serve as predictor for changes in axial length that might be correlated with myopia progression. Optical coherence tomography (OCT) provides a tool for imaging the choroid, however, with certain difficulties because of a limited visibility of the scleral-choroidal interface. Considering the previously reported effect sizes of thickness change in human myopia research, this study investigated the repeatability of automated 3D choroidal segmentation across the macular area of 6 × 6 mm2. Fifteen subjects underwent nine volume scans in two OCT devices with analysis of the 95% interval of repeatability, intersubject and intrasubject variations, as well as interdevice agreement. Repeatability generally improved with increasing eccentricity from the fovea. The nasal perifoveal region exhibited the best repeatability with ±19 and ±21 μm in both OCT devices, whereas the subfovea showed a repeatability of ±57 and ±44 μm, respectively. High inter- and intrasubject variations were observed, together with a negative bias in the device agreement. Although there is still limited data on thickness changes of the nasal choroid, future studies could focus more on measuring the effect size in the nasal perifoveal area to account for metrological issues in choroidal segmentation.