This research demonstrates the use of an unmanned aerial vehicle (UAV) to characterize the gaseous (CO2) and particle (10–500 nm) emissions of a ship at sea. The field study was part of the research voyage “The Great Barrier Reef as a significant source of climatically relevant aerosol particles” on board the RV Investigator around the Australian Great Barrier Reef. Measurements of the RV Investigator exhaust plume were carried out while the ship was operating at sea, at a steady engine load of 30 %. The UAV system was flown autonomously using several different programmed paths. These incorporated different altitudes and distances behind the ship in order to investigate the optimal position to capture the ship plume. Five flights were performed, providing a total of 27 horizontal transects perpendicular to the ship exhaust plume. Results show that the most appropriate altitude and distance to effectively capture the plume was 25 m a.s.l. and 20 m downwind. Particle number emission factors (EFPNs) were calculated in terms of number of particles emitted (no.) per weight of fuel consumed (kgfuel). Fuel consumption was calculated using the simultaneous measurements of plume CO2 concentration. The calculated EFPN was 7.6±1.4×1015no. kgfuel-1 which is in line with those reported in the literature for ship emissions ranging from 0.2 to 6.2×1016 no. kgfuel-1. This UAV system successfully assessed ship emissions to derive EFPN under real world conditions. This is significant as it provides a novel, relatively inexpensive and accessible way to assess ship EFPN at sea.