Born and raised in Chester, Vermont, Hager received a common school education. In 1856, he was appointed assistant naturalist of Vermont. He was assistant state geologist under Edward Hitchcock 1857-1861, and state geologist and curator of the state cabinet of natural history 1862-1870. In 1870, he was appointed state geologist of Missouri, and in 1877 he became librarian of the Chicago Historical Society. Hager was commissioner from Vermont to the Paris Exposition of 1867.