 From 1890 to 1891, he was a professor of pedagogy at the State University of Iowa (now known as the University of Iowa), after which he took the position of superintendent in Des Moines beginning in 1891.

Cooper served as president of the Iowa State Teachers' Association in 1893 and used his position to argue for more rigorous training of teachers in the state.He observed that "it is a well-known fact, not flattering to be sure, that a first grade certificate in Iowa is about equal in grade to the second-class certificate in Illinois, Wisconsin, Indiana, Minnesota, and other sister states.