The association between pupillary responses to repeated stimuli and adult refractive error has been previously demonstrated. This study evaluated whether this association exists in children and if it varies by season. Fifty children aged 8–17 years (average: 11.55 ± 2.75 years, 31 females) with refractive error between + 1.51 and − 5.69 diopters (non-cycloplegic) participated (n = 27 in summer, and n = 23 in winter). The RAPDx pupilometer measured pupil sizes while stimuli oscillated between colored light and dark at 0.1 Hz in three sequences: (1) alternating red and blue, (2) red-only, and (3) blue-only. The primary outcome was the difference in pupillary responses between the blue-only and red-only sequences. Pupillary constriction was greater in response to blue light than to red for those with shorter eyes in summer (β = − 9.42, P = 0.034) but not in winter (β = 3.42, P = 0.54). Greater constriction comprised faster pupillary escape following red light onset and slower redilation following stimulus offset of both colors (P = 0.017, 0.036, 0.035 respectively). The association between axial length and children’s pupillary responses in summer, but not winter may be explained by greater light-associated release of retinal dopamine in summer. Shorter eyes’ more robust responses are consistent with greater light exposure inhibiting axial elongation and reducing myopia risk.