Ekelöf grew up in an upper-class Stockholm home with a syphilitic father from whom the mother divorced. After graduating, he pursued oriental studies in London, which he continued in Uppsala. They established a deep familiarity especially with Arabic and Persian culture. Trips to France brought him into contact with surrealist poetry and modernist art and music. Ekelöf lost his wealth in the Kreuger crash in 1932 and was forced to feed on reviews and art critics.

His translations include both poems by Ibn al-‘Arabí and anthologies of French poetry, esp. French surrealism. In his writings he moved on from romanticism to a more existential sphere on the borders of mysticism and metaphysical poetry.

Gunnar Ekelöf made his debut in 1932 with the poetry collection "Late on Earth” (sent på jorden). After three more poetry collections, which he partly renounced, his big breakthrough came in 1941 with the poetry collection "Ferry Song” (Färjesång) (1941), while he further established his name with the socially critical poetry collection "Non Serviam" (1945). The major achievement in his late work came in 1965-67, with the publication of the large-scale Akrit trilogy, consisting of three suites written partly under the influence of his great interest in the Orient and Byzantine history. For the first part of the trilogy, "Diwan over the Prince of Emgión", Ekelöf was awarded the Nordic Council's Literature Prize in 1966.

In 1938 he made a pilgrimage to Raivola, the homestead of late Edith Södergran in Karelia, together with Finnland-Swedish poet Elmer Diktonius.