Up to 75% of pre-hospital trauma patients experience moderate to severe pain but this is often poorly recognised and treated with insufficient analgesia. Using multi-level logistic regression analysis, we aimed to identify the determinants of pre-hospital analgesia administration and choice of analgesic agent in a single helicopter-based emergency medical service, where available analgesic drugs were fentanyl and ketamine. Of the 1156 patients rescued for isolated limb injury, 657 (57%) received analgesia. Mean (SD) initial pain scores (as measured by a numeric rating scale) were 2.8 (1.8), 3.3 (1.6) and 7.4 (2.0) for patients who did not receive, declined, and received analgesia, respectively (p < 0.001). Fentanyl as a single agent, ketamine in combination with fentanyl and ketamine as a single agent were used in 533 (84%), 94 (14%) and 10 (2%) patients, respectively. A high initial on-scene pain score and a presumptive diagnosis of fracture were the main determinants of analgesia administration. Fentanyl was preferred for paediatric patients and ketamine was preferentially administered for severe pain by physicians who had more medical experience or had trained in anaesthesia.