AIM: To investigate the changes in the choroidal thickness in healthy pediatric children in a longitudinal study, and to determine the ocular and systemic parameters that were significantly correlated with the changes in the choroidal thickness. METHODS: This study included 64 eyes of 34 healthy Japanese children with a mean age (±SD) of 4.4 (±0.4)y (range, 3.6-5.8y) at baseline. Swept-source optical coherence tomography (SS-OCT) was used to record images of the retina and choroid at the baseline and after a mean follow-up period of about 1.5y. The 3D raster scan protocol was used to construct the choroidal thickness map. Mean choroidal thickness was calculated for each of the nine sectors of the Early Treatment Diabetic Retinopathy Study grid. Best-corrected visual acuity, axial length, body height, and weight were also measured. Changes in measurements were defined as the baseline values subtracted from the values at the final visit. A generalized estimating equation was used to eliminate the effect of within-subject intereye correlations. RESULTS: The mean central choroidal thickness was significantly reduced during the follow-up period (baseline, 301.8±8.6 μm; final visit, 286.6±8.0 μm, P<0.001). The decrease in the choroidal thickness was greatest in the central sector, followed by the sectors of the inner and outer rings. The inner and outer rings had diameters of 1 to 3 mm and 3 to 6 mm, respectively. The changes in the choroidal thickness in the central, inner ring, and outer ring sectors were significantly and negatively correlated with the age, baseline body height, baseline body weight, and elongation of the axial length. CONCLUSION: These results indicate that the choroidal thickness among preschool-aged Japanese children decreased significantly during the follow-up period. The choroidal thinning is significantly associated with the elongation of axial length. These characteristics should be considered in the evaluation of choroidal thickness in younger children with retinochoroidal disorders.