Premenstrual syndrome (PMS) that occur during late luteal phase is a problem for many female athletes. Many studies reported that subjective condition is affected by PMS in female athletes. Moreover, female athletes with PMS have higher stress and/or anxiety levels during luteal phase compared with non-PMS athletes. However, the relationship between PMS and physical performance in female athletes are not clarified yet. The purpose of this study was to investigate the relationship between premenstrual syndrome (PMS) and jump performance in female track and field athletes. Sixteen participants who has natural basal body temperature pattern with the menstrual cycle (observed low-temperature and high-temperature phase), were participated in this study. PMS was assessed by ACOG’s premenstrual syndrome questionnaire. As physical performance, counter movement jump (CMJ) and rebound jump (RJ) were evaluated in low-temperature phase and high-temperature phase. The result of this study, no significant differences were observed in body composition and physical performance between low-temperature phase and high-temperature phase. However, compared with participants who had non-symptom, participants who had a breast tenderness of PMS showed larger decreases in jump height of CMJ (p = 0.038) and RJ index (p = 0.015) in high-temperature phase. Therefore, PMS may have a negative effect on physical performance during high-temperature phase in female athletes.