Balaenoptera borealis is a baleen whale and can be recognised as such by the plates of baleen (rather than teeth) suspended from the upper jaw and the two blowholes on the upper body. The sei whale is slender bodied and can reach up to 16 m in length. It is a member of the rorqual family with the characteristic ventral pleats of skin under the eye and the relatively flat and broad jaw. The ventral pleats do not extend up to the navel but end near the pectoral fin. The flippers are a uniform dark colour and the upper body is a uniform blue-grey colour. The sei whale has a dorsal fin rising at a steep angle on the back. It has a single prominent ridge on the snout.

At a glance, the sei whale can be easily be confused with the minke whale Balaenoptera acutorostrata but can be distinguished by having dark coloured flippers and a uniform blue-grey upper body. The sei whale can also be differentiated from Bryde's whale Balaenoptera edeni by having only a single prominent ridge on the rostrum.

Sei whales usually congregate in small groups of up to 5 individuals, although in feeding areas up to 30 have been seen together. It seldom breeches, and when diving, it does not show the tail flukes. It can remain submerged for up to 20 minutes (Kinze, 2002).