The Short-finned Pilot Whale has been exploited for centuries in the western North Pacific. The largest catches have recently occurred off Japan, where small coastal whaling stations and drive fisheries take a few hundred annually. In recent years, the southern form continues to sustain a higher kill than the northern form and is considered depleted The current annual national quota is 50. In 1982, the drive fishery at Taiji expanded and harpooning of the northern form was resumed off Sanriku and Hokkaido. Between 1982 and 1985, 1,755 whales of the southern form were killed, and 519 of the northern form were taken during this same period. The current annual national quota is 450. From 1985 to 1989, Japan took a total of 2,326 short-finned pilot whales. The drive fisheries in Japan, as well as the Japanese harpoon fishery continue today. In 1997, Japan recorded a catch of 347 Short-finned Pilot Whales (Olson and Reilly 2002).

A small, intermittently active fishery takes around 220 pilot whales per year at St. Vincent, and there are reports of a small fishery at St. Lucia (Bernard and Reilly 1999). Reliable catch data are not available for these Caribbean hunts. The species is also hunted in Indonesia and Sri Lanka, also with no regular reporting of catch levels.

Dolar et al. (1994) reported on directed fisheries for marine mammals in central and southern Visayas, northern Mindanao and Palawan, Philippines. Hunters at four of the seven investigated fishing villages took cetaceans for bait or human consumption, including short-finned pilot whales. These are taken by hand harpoons or, increasingly, by togglehead harpoon shafts shot from modified, rubber-powered spear guns. Around 800 cetaceans are taken annually by hunters at the sites investigated, mostly during the inter-monsoon period of February–May. Dolphin meat is consumed or sold in local markets and some dolphin skulls are cleaned and sold as curios. Although takes and possession were banned in December 1992, the ban did not stop dolphin and whale hunting, but it seems to have decreased the sale of dolphin meat openly in the market.

In U.S. Atlantic waters, pilot whales have been taken in a variety of fisheries (Olson and Reilly 2002). Based on preliminary data, the squid round-haul fishery in southern California waters is estimated to have taken 30 Short-finned Pilot Whales in one year. In the California drift gill net fishery between 1993 and 1995, the mean annual take of Short-finned Pilot Whales was 20 (Bernard and Reilly 1999). About 4 individuals/year are killed in the Hawaii-based long-line fishery (Forney and Kobayashi 2005). Such interactions have also been recorded in the western tropical Indian Ocean (Indian Ocean Tuna Commission, unpublished data). On the other side of the Pacific Ocean, an estimated 350 - 750 G. macrorhynchus die annually in passive nets and traps set in a Japanese fishery (Bernard and Reilly 1999) and an unknown number are taken incidentally by the large-mesh pelagic driftnets off eastern Taiwan. The most common human-related cause of death observed in waters off Puerto Rico and the US and British Virgin Islands were entanglement and accidental captures, followed by gunshots and spear wounds (Mignucci et al. 1999).

This species, like beaked whales, is likely to be vulnerable to loud anthropogenic sounds, such as those generated by navy sonar and seismic exploration (Cox et al. 2006). While conclusive evidence of cause and effect are often lacking, mass stranding events have been spatially and temporally associated with high levels of anthropogenic sound for Short-finned Pilot Whales (Hohn et al. 2006). Around Taiwan and adjacent areas, a series of unusual strandings of short-finned pilot whales coincided with large-scale military exercises in 2004 but whether these strandings were related to the exercises is unknown (Wang and Yang 2006).

Predicted impacts of global climate change on the marine environment may affect short-finned pilot whales, although the nature of impacts is unclear (Learmonth et al. 2006).