Helicopter-based shooting using either a .308 semi-automatic rifle or a semi-automatic 12-gauge shotgun is widely used to manage non-native ungulate populations in Australasia, but the animal welfare outcomes of these two firearms have not been robustly compared. We conducted a randomised field study to compare the animal welfare outcomes of helicopter-based shooting of fallow deer (Dama dama) using a shotgun with three types of lead-based shot (Winchester® 00 Buck, 1 Buck or 4 Buck) relative to a .308 rifle with 135-grain lead-based bullets in New South Wales, Australia, in 2023. All deer that were shot at (n = 390) were killed. Time-to-event curves for times from pursuit to first shot, first shot to insensibility, and the sum of these two metrics (‘total time’), were similar among the four ammunition types. The mean number of shots fired per deer was similar across all four ammunition types, but the mean number of wound tracts per deer increased across the four ammunition types with the number of projectiles per cartridge. All deer subjected to post mortem examination had $ \ge $ 1 wound tract or projectile in the thorax. Our study indicates that using a .308 semi-automatic rifle or a 12-gauge semi-automatic shotgun for helicopter-based shooting of non-native deer, when the latter is used at ranges ≤ 30 m, provides similar animal welfare outcomes.