Freeman was born in Rutland, Vermont in 1826. After receiving private tutelage from a local reverend, William Mitchell, Freeman attended Middlebury College, where he graduated as salutatorian in 1849. The following year, he moved to Pittsburgh, Pennsylvania, to take up a position as professor of science and mathematics at the Allegheny Institute (later Avery College), a new state-chartered college founded to educate free African Americans. He was named president of the college in 1856.
Dr. Russell Irvine of Georgia State University, author of The African American Quest for Institutions of Higher Education Before the Civil War: The Forgotten Histories of the Ashmun Institute, Liberia College, and Avery College (2010), wrote the first biography of Martin Henry Freeman. Titled Martin H. Freeman of Rutland: America's First Black College Professor and Pioneering Black Social Activist (1996), it was first published as an article in Volume XXVI, Number 3 of the Rutland Historical Society Quarterly and later appeared in Professor Irvine's book, The History of Black Higher and Professional Education.