Seeger was born in New York and grew up in Maryland and Washington D.C. His father, Charles Louis Seeger Jr., was a composer and pioneering ethnomusicologist, investigating both American folk and non-Western music. His mother, Ruth Crawford Seeger, was a composer. His eldest half-brother, Charles Seeger III, was a radio astronomer, and his next older half-brother, John Seeger, taught for years at the Dalton School in Manhattan. His next older half brother was Pete Seeger. His uncle, Alan Seeger, a poet, was killed during the First World War. His sister Peggy Seeger, also a well-known folk performer, was married for many years to British folk singer Ewan MacColl. His sister, singer Penny Seeger, married John Cohen, a member of Mike's musical group, New Lost City Ramblers. Seeger was a self-taught musician who began playing stringed instruments at the age of 18. He also sang Sacred Harp with Ewan and Calum MacColl.
The family moved to Washington D.C. in 1936 after his father's appointment to the music division of the Resettlement Administration. While in Washington D.C., Ruth Seeger worked closely with John and Alan Lomax at the Archive of American Folk Song at the Library of Congress to preserve and teach American folk music. Ruth Seeger's arrangements and interpretations of American Traditional folk songs in the 1930s, 1940s and 1950s are well regarded.
At about the age of 20, Mike Seeger began collecting songs by traditional musicians on a tape recorder. Folk musicians such as Lead Belly, Woody Guthrie, John Jacob Niles, and others were frequent guests in the Seeger home.
In 1958 he co-founded the New Lost City Ramblers, an old-timestring band in New York City, during the Folk Revival. The other founding members included John Cohen and Tom Paley. Paley later left the group in 1962 and was replaced by Tracy Schwarz. The New Lost City Ramblers directly influenced countless musicians in subsequent years. The Ramblers distinguished themselves by focusing on the traditional playing styles they heard on old 78rpm records of musicians recorded during the 1920s and 1930s. Tracy was also in Mike's other band, Strange Creek Singers. So was Mike's former wife, Alice Gerrard. She was Alice Seeger in that band and sang and played guitar in it. The other people in Strange Creek Singers were bass player and singer Hazel Dickens and banjo player Lamar Grier who didn't sing at all. Mike sang and played guitar, banjo, fiddle, mandolin, autoharp, and harmonica in the band.