Founded in 1968 by Dr. Walter Turnbull, the choir also founded as The East Harlem Boy's Choir, at the Ephesus Seventh-day Adventist Church in Harlem, grew to be more than just a performing group. The Choir Academy of Harlem has been for years a school overseen by the New York City Department of Education and had at its peak a student body of over 500 boys and girls. The Boy's Choir of Harlem was evicted from this establishment in early 2006.

The choir is internationally known. Performers receive rigorous voice training and perform many types of music, including classical, hip-hop, r&b, jazz, and gospel music. Over 150,000 people see the choir live each year across the United States as well as in Canada, France, Japan, the Netherlands, and the United Kingdom. The BCH were also the recipients of a Grammy.

The choir has performed on soundtracks for films including Glory , Malcolm Xand many Spike Lee films and has performed for Presidents at the White House, and dignitaries at the United Nations. It also performed live for the visits of Nelson Mandela and Pope John Paul II. It performed on Chicago rapper Kanye West's song, Two Words, and Jesus Walks. The choir also performed America the Beautiful to open Wrestlemania XX. Their glorious voices have also appeared on albums with Kathleen Battle, Luciano Pavarotti, Quincy Jones and many more.

The choir for many years enjoyed the sponsorship of the City of New York, which gave them free use of the Arthur Schomburg School on East 127th Street in Harlem. However, the choir has lost this support through a series of scandals. First, a lack of financial controls led to the program's running up a $5 million deficit. Second, in 2001, the choir's chief counselor sexually abused a student, and Dr. Turnbull did not fire him or report the abuse to authorities. As a result, in early 2006, the Dr. Turnbull and other choir staff were kicked out of their long-time home.

Choir Member Rashad Allen says "the choir means more to me than anything, it has taught me certain things and aspects of life that the streets of Harlem would've not given, and I thank Dr. Walter J. Turnbull so much for believing in my gift and talent".

The Choir has now relocated to the Metropolitan Community Methodist Church, where the 40 boy choir rehearses and prepares for upcoming events. The Choir's star soloists are Justin Austin, and Darnelle Watts. The Boys Choir of Harlem has also created many successful alumni like M. Roger Holland, Kelis (of The Girls Choir of Harlem) and many people now involved with music industry.

The majority of the choir's members are African American and Hispanic.