Background: Menstrual cycle and premenstrual syndrome (PMS) refer to the periodic recurrence of a combination of physical, psychological, and behavioral changes in women. Objectives: The aim of this study was to determine the relationship between the age at menarche and PMS with anthropometric indices in the high school female students in Zahedan, Iran. Methods: This descriptive-analytical study was performed on 300 high school female students in Zahedan in 2017. The demographic and anthropometric characteristics of the participants were recorded. The standard PMS questionnaire was used to study PMS. Data were analyzed by SPSS version 22 using descriptive statistics (mean and standard deviation) as well as analytical statistics, including t-test and Pearson's correlation test. A value of P < 0.05 was considered significant. Results: The results showed that 221 subjects (73.7%) had PMS, whereas 79 subjects (26.3%) had no syndrome. There was a significant correlation between the mean age at menarche and weight (P = 0.004) as well as height (P = 0.025). A significant difference was observed in terms of the status physical factors (P = 0.038), between the mild and severe forms of PMS and age at menarche (P = 0.03). Conclusions: Given the high prevalence of PMS and its association with anthropometric indices, it is suggested to improve the nutritional status and physical health of high school female students.