Joining the English faculty after graduation, Lyons became one of Notre Dame's most popular professors, lived with students in a campus dormitory, and continued to contribute to the literary and spiritual life of the students. He was known for welcoming all students for informal discussions in his small room in the old administration building. For more than a quarter century, "Lyons actively participated in the building of Notre Dame as a academic institution. In an era which lacked qualified lay teachers, he became the heart and soul of the Notre Dame faculty. Lyons was a man respected not only for his teaching ability, but also for his genuine concern for students."
Professor Lyons died after a long illness on August 22, 1888, and was remembered at his funeral as a "bright example of energy and perseverance" who dedicated his life in service to the students of Notre Dame. (Source: Jon Pepetti, "Lyons left behind more than just a dorm," The Observer, November 8, 1991.)