Purpose <p>To assess the alterations in corneal topography with either 1% or 0.01% atropine treatment in myopic children.</p> Methods <p>This 6-month randomized controlled trial enrolled myopic children aged 6–12 years and randomly allocated them to group A (<i>n</i> = 92; 1% atropine once weekly) or group B (<i>n</i> = 85; 0.01% atropine once daily). Scheimpflug imaging was performed at baseline, 1 week, 3 months, and 6 months post-administration.</p> Results <p>In group A, a significant hyperopic shift (0.29 D) and progression of cylinder refraction (-0.10 D) were occurred. This cylindrical change exhibited a positive correlation with posterior corneal astigmatism. In group B, myopia progression was observed (-0.25 D), but the cylinder refraction changes were not significant (-0.04 D). A significant reduction in anterior keratometry (-0.08 D) and a concomitant increase in posterior corneal astigmatism (0.04 D) were documented. Furthermore, cylindrical change exhibited inverse associations with younger age, spherical refraction, and posterior corneal astigmatism. Changes in posterior corneal asphericity (Q-value) were inversely correlated with spherical refraction. Moreover, both groups exhibited significant posterior Q-value flattening (-0.13 and − 0.15, respectively), and changes in posterior K1 and K2 were positively correlated with the Q-value change.</p> Conclusion <p>We found that 1% or 0.01% atropine had a minor impact on the corneal topography. Longitudinal alterations in corneal geometry are predominantly ascribable to physiological ocular growth and myopic progression rather than to atropine exposure.</p> Trial registration number <p>Clinical Trials.gov PRS (Registration No. NCT03949101). Registration Date: 2019-05-11</p>