Choroidal thickness is associated with many ocular conditions, interchangeability among different generations of optical coherence tomography is therefore important for both research purpose and clinical application. Hence, we compared choroidal thickness measurements between spectral-domain optical coherence tomography (SD-OCT) and swept-source optical coherence tomography (SS-OCT) in healthy paediatric eyes. A total of 114 children from the population-based Hong Kong Children Eye Study with mean age of 7.38 ± 0.82 years were included. Choroidal thickness of the right eye was measured by both devices. The central foveal choroidal thickness (CFCT) measured by SD-OCT and SS-OCT was 273.24 ± 54.29 μm and 251.84 ± 47.12 μm respectively. Inter-device correlation coefficient was 0.840 (95% CI 0.616-0.918). However, choroidal thickness obtained by SD-OCT was significantly thicker than that measured by SS-OCT with a mean difference of 21.40 ± 33.13 μm (P < 0.001). Bland-Altman limit of agreement on the relative difference scale for SD-OCT/SS-OCT was 86.33 μm. Validated conversion equation for translating SD-OCT CFCT measurement into SS-OCT was SS-OCT = 35.261 + 0.810 × SD-OCT. In conclusion, intra-class correlation coefficient (ICC) shows an acceptable agreement between SD-OCT and SS-OCT, however, there was a significant inter-device difference of choroidal thickness measurements in normal children eyes. Therefore, the measurements are not interchangeable.