Killer whale (Orcinus orca) is frequently encountered in coastal and high productive pelagic waters, near the shelf break. In the south-western Atlantic Ocean, spatial and temporal occurrence patterns are poorly known. However, the monitoring of the interaction between killer whales and longline fishery suggests that the species is frequent in this region. We analysed the killer whale presence within the Uruguayan pelagic longline fishing zone. Data were collected from 1996 to 2007, during 2189 fishing events, by vessel skippers and on-board observers. We estimated the sighting rate (SR = sightings days/fishing days * 100) for different time scales and in 1 × 1 degree grids. Generalized linear models were used to evaluate the effect of spatial, temporal, environmental and operational variables on the species presence. Killer whales were sighted in 100 fishing days (SR = 4.5%), this occurrence being explained by distance from shore and sea surface temperature, varying among months and fishing boats. Although sightings occurred year round, they were more frequent in autumn and winter, at 150–400 nautical miles (nm) from shore (mean = 250 nm) and in waters with temperatures ranging from 19 to 24°C (mean = 22°C). Sets took place between 19°–40°S and 21°–54°W, while killer whales occurred mostly from 34°–37°S and 48°–53°W. In this region, the high productive Brazil—Malvinas Confluence Zone is located, and concentrates fishing effort and also killer whales.