The grey-headed fish eagle is a striking bird and an impressive hunter, with a relatively small head, longish neck and a powerful, grey beak. The plumage is brownish-grey on the upperparts and white below. It has relatively short legs, a rounded tail, sandy-yellow eyes, and long, black talons. The female grey-headed fish eagle is usually larger and heavier than the male, and juveniles can be recognized by the white belly mottled with brown.

The grey-headed fish eagle is sometimes mistaken for the lesser fishing eagle (Ichthyophaga humilis); however, the grey-headed fish eagle can be distinguished by its darker, duskier plumage and its tail, of which the last two-thirds of the tail are white, compared to the lesser fishing eagle which has a darker tail with no obvious white banding.

The calls of the grey-headed fish eagle include loud gurgles to the tune of awh-awhr and chee-warr repeated five to six times, and owlish oo-wooks. Somewhat disturbingly for other jungle inhabitants, the vocal range of this bird also includes a high-pitched scream.