Nearly 80% of new cases of myopia arise between 9 and 13 years old when puberty development also progresses rapidly. However, little is known about the association between myopia and puberty. We aim to evaluate the association between myopia and menarche, the most important puberty indicator for girls, and to test whether menarche could modify the effects of myopia-related behaviors. The participants came from two consecutive national surveys conducted in 30 provinces in mainland China in 2010 and 2014. We included 102,883 girls (61% had experienced menarche) aged 10–15 years. Risk behaviors for myopia which included sleep duration, homework time, and outdoor activity were measured by self-administrated questionnaire. Myopia was defined according to a validated method, and its relationships with menarche status and behaviors were evaluated by robust Poisson regression models based on generalized estimated equation adjusting for cluster effect of school. We found that postmenarche girls were at 13% (95% confidence interval: 11%–16%) higher risk of myopia than premenarche girls, after adjusting for exact age, urban–rural location, survey year, and four behavioral covariates. Short sleep duration (<7 h/d), long homework time (>1 h/d) and low frequency of weekend outdoor activity tended to be stronger (with higher prevalence ratios associated with myopia) risk factors for myopia in postmenarche girls than in premenarche girls, and their interaction with menarche status was all statistically significant (P < 0.05). Overall, our study suggests that menarche onset may be associated with increased risk of myopia among school-aged girls and could also enhance girls’ sensitivity to myopia-related risk behaviors.