Lyons was at Boston College for only a short while, before being appointed the rector of Gonzaga College. He assumed the position on December 27, 1908, succeeding Joseph J. Himmel. Shortly after he took office, an earthquake struck Messina, Italy, and the school offered a solemn high requiem mass for the victims, which was celebrated by Bishop Diomede Falconio and sung by Bonaventura Cerretti. In attendance were Bishop Denis J. O'Connell, Attorney General Charles Joseph Bonaparte, the Italian ambassador to the United States, Joseph Himmel, and priests from the Dominican, Franciscan, and Paulist orders. A banquet was held to honor the new president on February 10, which was attended by Congressman William Bourke Cockran. Lyons' term came to an end on July 8, 1909, when he was succeeded by Eugene DeL. McDonnell.