Objectives Transport destination decisions by prehospital personnel depend on a combination of protocols, judgment, patient acuity, and patient preference. Non-protocolized transport outside the service area may result in unnecessary time out of service and inappropriate resource utilization. Scant research exists regarding clinician rationale for destination decisions. Methods We retrospectively reviewed one year of scene transports by a single rural, hospital-based emergency medical services (EMS) system. We collected dispatch, patient demographic, primary impression, and transport data from prehospital records and matched them to emergency department (ED) data. We characterized rationale for transport decisions and compared rates of hospital admission and specialist consultation in the ED as surrogates for decision appropriateness. Results We reviewed 2,223 patient transports, 281 of which were transported out of the service area. The most common reasons for out-of-area transport were patient preference NOT related to prior medical care (40%) and clinician judgment (24%). Admit rates were highest for per protocol (85%) and patient preference related to prior medical care (67%) groups and lowest for no explanation (41%) and clinician judgment (47%) groups. Rates of in person specialist consultation in the ED were highest in per protocol (69%) and clinician judgment (47%) groups and lowest in no explanation (23%) and patient preference NOT related to prior medical care (30%) groups. Clinician judgment was less predictive of admission and specialist consultation for non-trauma and pediatric patients than for all patients. Median time out of service was more than twice as long for out-of-area transports (140 min) compared to patients transported to the nearest facility (62 min). For out-of-area transports discharged from the ED without specialty consultation (n = 104), ambulances traveled an additional 52 miles/patient compared to theoretical transport to nearest facility. Conclusions Unit out of service time more than doubled for non-protocolized transports outside of the service area and rationale for destination decisions variably predicted admission and specialist consultation rates. Patient preference NOT related to prior medical care and, in pediatric and non-trauma populations, clinician judgment, were less predictive of admission and specialist consultation. Transport guidelines should balance rationale for transport destination and patient characteristics with resource preservation, especially in low-resource systems.