At Columbia, Kilmer was vice-president of the Philolexian Society (a literary society), associate editor of "Columbia Spectator" (the campus newspaper), and member of the Debating Union. He completed his Bachelor of Arts (A.B.) degree and graduated from Columbia on May 23, 1908. Shortly after graduation, on June 9, 1908, he married Aline Murray (1888–1941), a fellow poet to whom he had been engaged since his sophomore year at Rutgers. The Kilmers had five children: Kenton Sinclair Kilmer (1909–1995); Rose Kilburn Kilmer (1912–1917); Deborah ("Sister Michael") Clanton Kilmer (1914–1999) who was a Catholic nun at Saint Benedict Monastery in St. Joseph, Minnesota; Michael Barry Kilmer (1916–1927); and Christopher Kilmer (1917–1984).