In 1941 he joined the staff of the Rijksmuseum van Natuurlijke Historie in Leiden, where he was especially interested in fossil rhinoceroses and hippopotami.
In the same year he promoted under Professor Hilbrand Boschma (1893–1976) with his dissertation Prehistoric and fossil Rhinoceroses from the Malay Archipelago and India.
From 1950 to 1951 he got a Rockefeller fellowship and worked at the American Museum of Natural History in New York City.
Hooijer published 267 scientific articles about vertebrate fossils from Indonesia, Africa, the Near East (especially Israel), the Netherlands, the Antilles, and South America.
Many of these works were devoted to fossil rhinoceroses, cats, hogs, rodents, primates, and probiscoidae.