To determine the comparability of choroidal thickness (ChT) measurements using swept source (SS) and spectral domain (SD) optical coherence tomography (OCT) devices in patients with pachychoroid diseases. Patients with pachychoroid diseases were recruited. OCT scans were performed sequentially with a Cirrus HD OCT 5000 and Plex Elite 9000. Images were analyzed by two independent observers. Each image was independently measured twice by each observer to determine the intraobserver repeatability. A total of 55 eyes were included. The average ChT of the subfoveal area using SS-OCT and SD-OCT was 430.5 ± 68.1 and 428.5 ± 57.9 μm, respectively, which did not show a significant result as the main effect in the repeated-measure analysis of variance (P = 0.067). Using SS-OCT, the intraobserver intraclass correlation coefficient (ICC) of both observers was > 0.950 at every measured point, and the interobserver coefficient of repeatability (CR) of the subfoveal area was 45.1 μm (95% confidence interval (CI), 40.8-49.4). Using SD-OCT, the intraobserver ICC of both observers was > 0.800, and the interobserver CR of the subfoveal area was 71.2 μm (95% CI, 64.4-78.0). Additionally, the intraobserver and interobserver CRs showed significantly better repeatability in SS-OCT than SD-OCT in F-test. In patients with ChT ≥ 400 μm, the interobserver CRs of SS-OCT and SD-OCT were 48.4 (95% CI, 42.6-54.2) and 95.2 μm (95% CI, 83.9-106.6), respectively. In patients with a subfoveal active lesion, the interobserver CRs were 44.5 (95% CI, 37.6-51.4) and 100.1 μm (95% CI, 84.6-115.5), respectively. Although the ChT measurements were comparable between SS-OCT and SD-OCT devices in pachychoroid diseases, SD-OCT showed low reliability in patients with ChT ≥ 400 μm and subfoveal active lesions. SS-OCT would be therefore more suitable for observation and follow-up of choroidal structures in pachychoroid diseases.