A number of cetacean species are observed regularly offshore during the summer months and also from the 'Good Shepherd', Fair Isle's mail-boat, on its weekly crossing to Shetland.

Species regularly seen include:
Minke Whale (Balaenoptera acutorostrata)
Killer Whale (Orcinus orca)
White-beaked Dolphin (Lagenorhynchus albirostris)
Atlantic White-sided Dolphin (Lagenorhynchus acutus)
Risso's Dolphin (Grampus griseus)
Harbour Porpoise (Phocoena phocoena)

Other species which also occur in Fair Isle and Shetland waters are:
Long-finned Pilot Whale (Globicephala melas)
Fin Whale (Balaenoptera physalus)
Sperm Whale (Physeter catodon)
Humpback Whale (Megaptera novaeangliae)

This species is making a comeback into Shetland waters. Following the first sighting since the 1970's, off Buness in October 2004, another was seen in July 2005 and the recovery continued into 2006 with no less than four sightings - two together off the north end of Buness on 21st July followed by singles on 16th, 25th & 30th August.

Visitors in October 2014 had the added bonus of two humpback whales Megaptera novaeangliae close inshore off the south of the Isle. In recent years a humpback recovery has led to regular records in Shetland and the species has now found Fair Isle. The only previous recent record was of one breaching 25 km south-east of Fair Isle in 1994. Up to the early 20th century large whales were seen regularly passing the isle, including humpbacks.