Background Primary dysmenorrhea is a common gynecological condition that can negatively impact athletic performance in female athletes. Objective This study aimed to compare body composition, core stability, flexibility, balance, and psychological status in female athletes with and without primary dysmenorrhea (PD). Materials and methods Female athletes with (PD group, n = 51) and without (control group, n = 51) PD were included in the study. Body composition with bioelectrical impedance analysis technique, core stability with Mcgill trunk muscle endurance tests, flexibility with sit-reach test, balance with Y-balance test and psychological status with Athletic Psychological Skills Inventory (APSI) were assessed. Results Waist-hip ratio (p < 0.001) and body fat percentage (p = 0.010) values were higher in the PD group compared to the control group. However, trunk flexor muscle endurance test (p < 0.001) and trunk extensor muscle endurance test (p < 0.001), right and left trunk lateral flexor muscles (p < 0.001), Sahrmann test (p < 0.001), sit and reach test (p = 0.001) were lower in the PD group compared to the controls. However, there was no difference between the groups in terms of body water percentage, body muscle mass, body bone mass, balance score and APSI values (p > 0.05). Conclusion It was found that waist hip ratio and body fat percentage values of body composition parameters were higher and core stability and flexibility values were lower in female athletes with PD compared to without PD. Balance and pyshological status had no differences between groups. According to these results, additional training programs may be recommended to improve body composition, core stability and flexibility in female athletes with PD.