Recently, there has been a growing interest in relation to the female athlete, especially in widespread disciplines such as football. Concerns about vitamin D deficiency status have recently been considered due to its effects on the performance and health status of female footballers. However, its relationship to body composition and muscle damage in female football athletes remains unclear to date. The purpose of the present study was to analyse the association of the vitamin D status of Spanish elite female football players with anthropometric variables and markers of muscle damage. Ethical consent was obtained from a total of 21 players from a Spanish elite women’s football team (20–33 years). Anthropometric analysis was carried out according to the standardised protocol of the International Society for the Advancement of Kineanthropometry (ISAK). The clinical analyses, based on urine and blood samples, were carried out by the club’s medical staff at the start of the season in the early morning in a fasting state. The athletes were also asked about the regularity of their menstrual cycle and some dietary habits. Thirty-three percent of the female athletes had vitamin D levels below the reference values. Significantly higher FM values were observed in athletes with low vitamin D status (p < 0.05), as well as statistically significant negative correlations between vitamin D levels and FM (p < 0.05) in the group of female players with vitamin D levels below the baseline values. No significant associations were observed between markers of muscle damage and the other variables. Complementing an assessment of body composition with a biochemical analysis of vitamin D levels may be an interesting strategy in the process of monitoring the elite female football player throughout the season.