Anthropometric indices (AI) have been known to be associated with age at menarche (AAM). The aim of this longitudinal study was to evaluate the changes in AI and its association with AAM in a community-based population in Iran. From among 10,192 women, we included 6818, aged ≥ 10 years, who were post-menarche at the time of entering the study and their AAM ranged between 8 and 18 years. Study subjects were divided into groups by tertiles birth cohort (BC) (born ≤ 1939, 1940-1969, and ≥ 1970) and AAM (≤ 11, 12-15, and ≥ 16 years). Generalized estimating equation analysis was performed to evaluate the association between changes of AI in different BCs with AAM groups. Overall mean of AAM was 13.5 ± 1.4 years. Mean body mass index (BMI) was significantly increased over time more in those with early AAM (≤ 11 years) compared to those with AAM ≥ 16 years; changes in mean BMI of 1.24 kg/m (95% CI 0.32, 2.15), 2.61 kg/m (95% CI 1.90, 3.33), and 3.99 kg/m (95% CI 2.46, 5.51) in BC ≥ 1970, BC (1940-1969), and, BC ≤ 1939, respectively.Conclusion: Our findings showed an inverse association of AAM with mean BMI, waist to height ratio, and waist circumference, an association weaker in younger women compared to other age groups.What is Known:• Limited data are available on the association of menarcheal age with anthropometric indices.• Previous studies reported conflicting and inclusive results of this association.What is New:• Our results can provide beneficial information on the association of menarcheal age with anthropometric indices based on different age groups.• This long follow-up study shows an association of menarcheal age with anthropometric indices which are stronger in older women except for height.