To investigate the effect of orthokeratology (OK) lenses and that of 0.01% atropine eye drops on axial length (AL) elongation in children with myopic anisometropia. Methods: Ninety-five children with myopic anisometropia who used OK lenses (N¼49) or 0.01% atropine eye drops (N¼46) were enrolled in this retrospective 1-year study. For all children, the eyes with higher spherical equivalent refractive error (SER) were assigned to the H-eye subgroup, whereas the fellow eyes with lower SER were assigned to the L-eye subgroup. Results: After 1-year treatment, the mean change in the AL of H eyes and L eyes in the OK lenses group was 0.1860.16 mm and 0.2460.15 mm, respectively (P¼0.15), and 0.2860.20 mm and 0.2560.18 mm, respectively (P¼0.48), in the 0.01% atropine group. Multivariate regression analyses showed significant differences in AL change between H and L eyes after treatment with OK lens (P¼0.03), whereas no significant difference in the 0.01% atropine (P¼0.22). The change in the AL in the H-eye group was less with OK lenses than with 0.01% atropine (P¼0.04), whereas there was no significant difference between the change in AL in the L-eye group between treatment with OK lens and 0.01% atropine (P¼0.89). Conclusions: In myopic anisometropic children, AL differences between 2 eyes decrease by wearing OK lenses but do not change after administration of 0.01% atropine eye drops. The increased effect of OK lenses, but not 0.01% atropine, in reducing axial elongation at 1 year in the eye with higher SER in anisometropic children warrants further investigation.