Hamstring injuries are the most common injury sustained by Australian Football players. Eccentric training has been proposed as a potential preventative strategy. This pilot randomised controlled trial (RCT) evaluated the effectiveness of a pre-season eccentric training program for preventing hamstring injuries at the community level of Australian Football. Seven amateur clubs (n=220 players) were recruited. Players were randomised within clubs to the intervention (eccentric exercise) or control (stretching) groups and randomisation was stratified according to previous history of hamstring injury. Five exercise sessions were completed over a 12-week period, three during the pre-season and two during the first 6 weeks of the season. Compliance was recorded and players were monitored for the season to collect injury and participation data. There was no difference between the control (n=106) or intervention (n=114) groups with respect to baseline characteristics. Only 46.8% of all players completed at least two program sessions. Compliance was poorest for the intervention group. Intention-to-treat analysis suggested that players in the intervention group were not at reduced risk of hamstring injury (RR 1.2, 95% CI: 0.5, 2.8). When only control and intervention group players who participated in at least the first two sessions were analysed, 4.0% of intervention and 13.2% of control group players sustained a hamstring injury (RR 0.3, 95% CI: 0.1, 1.4; p=0.098). The findings suggest that a simple program of eccentric exercise could reduce the incidence of hamstring injuries in Australian Football but widespread implementation of this program is not likely because of poor compliance.