There is evidence showing that excessive mental stress is detrimental to the menstrual period, and it is known that many elite athletes are highly susceptible to mental anxiety. This study investigated the nutritional intake and mental anxiety of 104 relatively young elite endurance athletes aged 16 to 23 years and used a multiple logistic model to examine the factors that might be related to menstrual irregularity. Calcium intake was marginally associated with the occurrence of menstrual irregularities (odds ratio = 1.004, p = 0.030), whereas there were strong associations between body mass or state anxiety and menstrual irregularities in elite athletes (odds ratio = 0.557, p = 0.035 for body mass; odds ratio = 1.094, p = 0.006 for state anxiety). These results suggested that state anxiety would be an important factor causing menstrual irregularity in elite endurance athletes. It is recommended that elite athletes are monitored for anxiety levels and develop a strategy for stress management.