Seeger was born in Mexico City, Mexico, to American parents Elsie Simmons (née Adams) and Charles Louis Seeger. During the 1890s, the family lived in Staten Island, New York. Seeger graduated from Harvard University in 1908, then studied in Cologne, Germany and conducted with the Cologne Opera. Upon discovering a hearing impairment, he left Europe to take a position as Professor of Music at the University of California at Berkeley, where he taught from 1912 to 1916 before being dismissed for his public opposition to U.S. entry into World War I. His brother Alan Seeger was killed in action on July 4, 1916, while serving as a member of the French Foreign Legion. Charles Seeger then taught at Juilliard (originally the Institute of Musical Art) in New York from 1921 to 1933 and the New School for Social Research from 1931 to 1935.