The college was renamed "Juniata College" in 1894 for the nearby Juniata River, one of the principal tributaries of the Susquehanna River, due to a ruling at the Brethren Church's Annual Meeting against using the term "Brethren" in naming a school.
In 1895, Dr. Martin Grove Brumbaugh, an 1881 graduate from Brethren Normal (Huntingdon Normal), took over the active presidency of Juniata until 1910.