Limited research exists on the effects of menstrual phase on athletic performance in team sport athletes. In this case-study we investigated the potential effect of menstrual cycle phase on several physical qualities in rugby athletes. Four eumenorrhoeic female rugby athletes completed a battery of physical tests weekly for 5-9 weeks, including 10-m sprint, countermovement (CMJ) and drop (DJ) jumps, isometric mid-thigh pull (IMTP), and Bronco. Concurrently, athletes tracked their menstrual cycle with a smartphone application (FitrWomanTM). To investigate differences in physical performance between phases, data were allocated into four different menstrual phases at the date of each weekly test. A mixed linear model was created for each physical quality of interest. Mean changes between phases were estimated using magnitude-based inferences with 90% confidence intervals. Individual differences between the average score for each menstrual phase with the value predicted by the trend of the other three phases were also assessed. At a group-level, possible greater performances were observed in the CMJ during the late luteal phase compared with menstruation, in the DJ during late luteal compared with luteal, and in the IMTP during late luteal compared with follicular to ovulation (Δ% = 4.9-7.0%). A variety of responses were observed between individuals for all the tests conducted. Understanding and accounting for individual responses during the menstrual cycle will likely be beneficial to training prescription and interpreting performance monitoring results.