Winkler came to Cornell in 1985 as a lecturer after obtaining his Ph.D. in 1983 at U. C. Berkeley. He joined the Cornell faculty in Ecology and Systematics, later renamed the Department of Ecology and Evolutionary Biology. He was the director of the Cornell University Museum of Vertebrates, a member of the Administrative Board of the Cornell Laboratory of Ornithology and selected as a Stephen H. Weiss Presidential Fellow for teaching in 2007.

Golondrinas de las Americas use standardized protocols to better understand the breeding biology of the swallows in the genus Tachycineta and their aerial insect prey. They monitor the effects of weather and insect density on avian breeding at different latitudes across the Western Hemisphere and are pursuing studies of geographic variation in many aspects of swallow biology.