Background Head injuries in children are a common and potentially devastating presentation. The CareTrack Kids (CTK) study assessed care of Australian children aged 0–15 years, in 2012 and 2013, to evaluate the proportion in line with guideline-based indicators for 17 common conditions. Overall adherence to guideline-based recommended practice occurred 59.8% of care encounters (95% CI: 57.5–62.0), and 78.3% (95% CI: 75.1–81.2) for head injury. This paper presents results for head injury, at indicator level. Methods A modified version of the RAND-UCLA method of indicator development was used. Indicators, measurable components of a standard or guideline, were developed from international and national guidelines relating to head injury in children and were ratified by clinical experts using a Delphi process. Paediatric nurses extracted data from medical records from general practitioners (GPs), emergency departments (EDs) and inpatient wards in Queensland, New South Wales and South Australia, for children under 15 years receiving care in 2012–13. Our purpose was to estimate the percentage adherent for each indicator. Results The medical records of 629 children with head injury were examined. Fifty-one percent of children were under 5 years old, with more males (61%) than females. Thirty-eight indicators were assessed. Avoidance of nasotracheal airways (100%; 95% CI: 99.4–100) or nasogastric tubes (99.7%; 95% CI: 98.5–100) for children with a head injury had the highest adherence. Indicators relating to primary and secondary assessment of head injuries were mostly adhered to. However, adherence to other indicators was poor (e.g., documentation of the past history of children (e.g., presence or absence of seizures) before the injury; 29.9% (95% CI: 24.5–35.7)), and for others was difficult to estimate with confidence due to small sample sizes (e.g., Children with a head injury who were intubated had PaO2 above 80mm Hg; 56.0% (95% CI: 28.6–80.9)). Indicators guiding clinical decision making regarding the need for CT scan had insufficient data to justify reporting. Conclusion This study highlights that management of head injury in children mostly follows guidelines, but also flags some specific areas of inconsistency. Individual sites are encouraged to use these results to guide investigation of local practices and inform quality improvement endeavours.