In 1870 he received his degree, subsequently working as an assistant in the physiological institute at the University of Vienna.

During his career, he received honorary doctorates from the Universities of Leipzig and Athens.

He performed investigations of color contrast, hue adaptation, apparent motion and on the sensitivity of retinal regeneration.

[1][2] He explained how the compound eye functions, and in 1891, published "Die Physiologie der facettierten Augen von Krebsen und Insekten", describing the compound eye physiology of insects and crustaceans.

In 1899, Exner co-founded the Phonogrammarchiv in Vienna, an archive for recording acoustic phenomena for scientific purposes.