Spot Vision Screener (SVS) can conduct refraction tests for both eyes within a short period. This study aims to evaluate the refraction and pupil diameters of 3-year- and 1-month-old Japanese children using SVS in regular medical checkup. We examined 2438 eyes of 1219 children (age: 3-year- and 1-month) in Fujieda (Shizuoka, Japan) to assess their refraction and pupil diameters and eye-position screening conducted by SVS. SVS successfully measured 1217 children (99.8%). Regarding the right eye refraction, the spherical power was +0.70 ± 0.55 D (median, +0.75 D), and the cylindrical power was −0.67 ± 0.49 D (median, −0.50 D). The pupil diameter of the right eyes was 5.57 ± 0.79 (median, 5.60) mm. we could obtain a large number of basic data for 3-year- and 1-month-old Japanese children. However, refraction and pupil diameter of children were not normally distributed, so careful handling of children’s basic data on the eye is necessary.