Indigenous children experience a disproportionally high number of injuries, particularly in remote communities. This study aimed to investigate: (1) the causes of injury to children within three remote Indigenous communities of Cape York, Australia; (2) differences between communities; and (3) if strengthening of alcohol restrictions reduced the incidence of injury. An injury profile for children aged 0–14 years was constructed for the period 1 January 2006 to 31 December 2011 using clinical file audit data from Primary Health Care Clinics located in each community. Children aged <14 years were responsible for 1461 injury presentations among 563 individuals. Males were responsible for 58.7% of presentations and 38% (n = 214) of children presented on three or more occasions. The leading causes of injury were falls (including sports); cutting and piercing; animals, insects and plants; transport and assault. There were variations in the order of major injury causes across the three communities. As primary causes of injury, falls and transport-related injuries aligned with other child populations. Cutting and piercing; animals, insects and plants; and assault-related injuries were more prevalent compared with other child populations. There was a significant difference in injury rates between communities and no significant difference before and after the strengthening of alcohol restrictions.