The short-finned pilot whale is found worldwide in offshore tropical, subtropical and warm temperate waters. There are known populations in the North Atlantic, from the United States to northern South America, including the Gulf of Mexico, and east to Europe and Africa. These populations are thought to move south during the spring and late winter into the western North Atlantic.

Other populations are found in the Pacific Ocean, from the Gulf of Alaska south to Guatemala. The short-finned pilot whale is also reported from the western North Pacific in the Sea of Japan, as well as in the southern Red Sea and the Indian Ocean.

Two distinct populations of short-finned pilot whale found off northern and southern Japan show differences in their anatomy and genetics, and may potentially comprise more than one distinct species or subspecies. However, their exact taxonomy has yet to be confirmed.