PURPOSE. To determine the influence of choroidal boundary morphology on the accuracy of automated measurements of subfoveal choroidal thickness (SFCT) in swept source optical coherence tomography (SSOCT). METHODS. A retrospective image analysis of foveal-centered horizontal line scans from normal and diseased eyes using the Topcon DRI OCT-1 Atlantis SSOCT was conducted. Subfoveal choroid-scleral junction (CSJ) and retina-choroidal junction (RCJ) morphologies were graded by two observers. Automated SFCT (A-SFCT) was compared with manual SFCT (M-SFCT) measurements from Bruch’s membrane to the posterior limits of choroidal vessel, hyperreflective stroma, and hyporeflective lamina fusca. Agreement in boundary grading was assessed by Cohen’s kappa. A-SFCT and M-SFCT were compared using Bland-Altman analysis and paired t-tests. RESULTS. A total of 200 eyes of 100 patients with a mean (SD) age of 62 (18) years were included. The choroidal vessel, stromal, and lamina fusca boundaries were visible in 100%, 58%, and 38% of the eyes, respectively. Interobserver agreement in RCJ and CSJ grading was high (kappa = 0.974 and 0.851). Mean A-SFCT differed from M-SFCT by only 2 μm at posterior choroidal vessel boundary (P = 0.801). A-SFCT overestimated SFCT at the posterior vessel wall boundary by 17 μm (P = 0.026) and 23 μm (P = 0.001) in the presence of a visible posterior choroidal stroma and lamina fusca, respectively. CONCLUSIONS. Automated outer choroidal boundary segmentation tends to identify the posterior limit of the choroidal vessel. Agreement between A-SFCT and M-SFCT is reduced by the presence of posterior stromal layer and lamina fusca. A-SFCT should be interpreted with RCJ and CSJ boundary grading.