Born in Boston, Massachusetts, he attended the local public schools before entering the wool industry.

He continued the major construction plan of his predecessor, overseeing the completion of St. Mary's Hall and Alumni Field.

[3] As a young boy, he moved to South Boston and became a parishioner of the Church of Saints Peter and Paul.

During this time, he studied Latin on his own, and joined the Young Men's Catholic Association, which was founded by the Church of the Immaculate Conception in the South End of Boston.

[5] Following his exposure to the Jesuits at Immaculate Conception Church, Lyons joined the Society of Jesus, and his application was accepted by the provincial superior, Thomas J. Campbell.

He found his formation at Frederick difficult, and suffered a nervous breakdown during his juniorate, which affected his eyesight.

[6] Following his philosophical studies, Lyons was sent to Gonzaga College in Washington, D.C., where he taught chemistry to the high school students.

[7] Following his tertianship, Lyons was appointed a professor of philosophy and political economy at St. Francis Xavier College in New York City.

[8] 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.

[9] A banquet was held to honor the new president on February 10, which was attended by Congressman William Bourke Cockran.

[7] He maintained good relations with the two successive Archbishops of Philadelphia, Patrick John Ryan and Edmond Francis Prendergast throughout his term, and the Church of the Gesú prospered during this time.

[17] With construction already underway, he had architects modify the plan for St. Mary's Hall to add a fourth floor, as well as expand the size of the chapel to accommodate 250 people.

[17] Lyons believed that it was his duty to support President Woodrow Wilson during time of war, and he was appointed to the Military Commission of Massachusetts during 1915 and 1916.

After three years, Lyons returned to Boston College as a professor of metaphysics,[25] and as the head of the department of philosophy.

[26] Seeing insufficient dormitory space as the most pressing need on campus,[28] he oversaw the construction of the New North building in 1925, which was completed in June 1926 in the Colonial Revival style.

[28] Lyons modernized the curriculum, introducing an alternate course of study to the classical one, and allowing majors for upperclassmen.

[31] President Coolidge also appointed him to a federal commission that would plan the 150th anniversary of the Battle of Bunker Hill.

[32] Upon the end of his leadership of Georgetown, Lyons joined the Jesuit mission band in Boston, with which he traveled throughout New England, New York, and Maryland for eight years.

His health began to deteriorate in 1936, so the Jesuit superiors stationed him at Weston College as the spiritual father of the theology students.

[33] In 1938, having seemingly recovered, he went to Boston College High School, but proved unable to continue working.