Study aim: to test the hypothesis that an eccentric training programme applied on women football players would reduce the hamstring injury rate by improving thigh muscle balance and, particularly, hamstring strength. Material and methods: three football teams were recruited for this randomised controlled trial. They played in the first and second divisions in Spain. Players were randomised within clubs either to the intervention (eccentric exercises, n = 22) or control (control exercises, n = 21) groups, and randomisation was stratified according to previous history of thigh strains. The eccentric programme was divided into 3 phases, and each phase was composed of 7 weeks. Compliance level and all injuries were recorded throughout the season as well as training and game exposure times. Muscle strength and power of the lower extremities and flexibility of the hamstrings and lower back were measured before and after the intervention. Results: the risk for sustaining a hamstring strain (RSHS) was reduced by 81%. However, differences were not significant due to the low number of subjects (relative risk 0.19; 95% coefficient interval 0.02–1.50). The strength of the hamstrings decreased in both groups (p < 0.05), whereas sprint time was improved only in the intervention group (p < 0.05). Conclusion: the present findings suggest that a simple program of eccentric exercise could reduce RSHS.