Background. Hamstring injuries are the most common injury in Australian Rules football. It was the aims to investigate whether a sports chiropractic manual therapy intervention protocol provided in addition to the current best practice management could prevent the occurrence of and weeks missed due to hamstring and other lower-limb injuries at the semi-elite level of Australian football. Methods. Sixty male subjects were assessed for eligibility with 59 meeting entry requirements and randomly allocated to an intervention (n = 29) or control group (n = 30), being matched for age and hamstring injury history. Twenty-eight intervention and 29 control group participants completed the trial. Both groups received the current best practice medical and sports science management, which acted as the control. Additionally, the intervention group received a sports chiropractic intervention. Treatment for the intervention group was individually determined and could involve manipulation/mobilization and/or soft tissue therapies to the spine and extremity. Minimum scheduling was: 1 treatment per week for 6 weeks, 1 treatment per fortnight for 3 months, 1 treatment per month for the remainder of the season (3 months). The main outcome measure was an injury surveillance with a missed match injury definition. Results. After 24 matches there was no statistical significant difference between the groups for the incidence of hamstring injury (OR:0.116, 95% CI:0.013-1.019, p = 0.051) and primary non-contact knee injury (OR:0.116, 95% CI:0.013-1.019, p = 0.051). The difference for primary lower-limb muscle strains was significant (OR:0.097, 95%CI:0.011-0.839, p = 0.025). There was no significant difference for weeks missed due to hamstring injury (4 v14, 2:1.12, p = 0.29) and lower-limb muscle strains (4 v 21, 2:2.66, p = 0.10). A significant difference in weeks missed due to non-contact knee injury was noted (1 v 24, 2:6.70, p = 0.01). Conclusions. This study demonstrated a trend towards lower limb injury prevention with a significant reduction in primary lower limb muscle strains and weeks missed due to non-contact knee injuries through the addition of a sports chiropractic intervention to the current best practice management. Trial registration. The study was registered with the Australian and New Zealand Clinical Trials Registry (ACTRN12608000533392).