The purpose of the current study was to investigate the effect of topical atropine on choroidal thickness using spectral-domain optical coherence tomography. A total of 30 healthy eyes from 30 children were analyzed in this study. A single drop of 1% atropine gel was administered twice daily for a week. Choroidal thickness (CT) was measured using SD-OCT, and changes in CT before and after administration of the eye drops were analyzed at the subfovea and at 1.0-mm intervals (up to 3.0 mm) from the fovea at superior, inferior, nasal, and temporal locations. Pre- and post-cycloplegic axial length (AL) was also measured using the IOLMaster. We observed that administration of 1% atropine gel led to a significant increase in the choroidal thickness under the fovea and at all intervals from the fovea. The greatest change in CT was observed in the inferior meridian, while the nasal meridian exhibited the least change. AL did not significantly differ before and after cycloplegia, and there was no significant correlation between the changes in AL and subfoveal CT. It was concluded that administration of 1% atropine gel can significantly increase CT in the eyes of young Chinese children, albeit with different magnitude at different locations.