Born in Hamburg, Meyer studied at the University of Leipzig, taught by Ernst Windisch from 1879. He received his doctorate for his thesis Eine irische Version der Alexandersage (an Irish version of the Alexander Romance) in 1884. He then took up the post of lecturer in Teutonic languages at the new University College, Liverpool, the precursor of the University of Liverpool, established three years earlier.
He continued to publish on Old Irish and more general Celtic language topics, as well as producing textbooks for the German language. In 1896 he founded, and jointly edited with Ludwig Christian Stern, the prestigious Zeitschrift für celtische Philologie.
In 1903 Meyer founded the School of Irish Learning in Dublin, and the next year created its journal Ériu, of which he was the editor. Also in 1904 he became Todd Professor in the Celtic Languages at the Royal Irish Academy. In October 1911 he followed Heinrich Zimmer as Professor of Celtic Philology at Friedrich Wilhelm University in Berlin; the following year a volume of Miscellany was presented to him by pupils and friends in honour of his election, and he was made a freeman of both Dublin and Cork. He also catalogued the various entries by different scribes in the Book of O'Donnell's Daughter, a 17th century manuscript written in Leuven and preserved in the Bibliothèque Royale in Brussels.
On the outbreak of the First World War, Meyer left Europe for the United States of America, where he lectured at Columbia, Urbana University, and elsewhere. A pro-German speech he gave in December 1914 to Clan na Gael on Long Island caused outrage in Britain and Ireland, and as a result he was removed from the roll of freemen in Dublin and Cork and from his Honorary Professorship of Celtic at Liverpool, and he resigned as Director of the School of Irish Learning and editor of Ériu.
Meyer remained in the United States and went on a lecture tour around the country. He was injured in a railway collision in 1915 and met 27 year old Florence Lewis while recovering in a California hospital. They married shortly afterwards. Florence went to Germany in 1916, Meyer in 1917. In 1919 Florence and her daughter went to Switzerland; Meyer died on 11 October, 1919, in Leipzig.
Miscellany presented to Kuno Meyer by some of his friends and pupils on the occasion of his appointment to the chair of Celtic philology in the University of Berlin; ed. by Osborn Bergin and Carl Marstrander. Halle: M. Niemeyer, 1912.