Boston's reputation as a higher education center derives in large part from the teaching and research activities of more than 100 colleges and universities located in the Greater Boston Area, with more than 250,000 students attending college in Boston and Cambridge alone.Within the city, Boston University exudes a large presence as the city's fourth-largest employer,and maintains a campus along the Charles River on Commonwealth Avenue and its medical campus in the South End. Northeastern University, another large private university, is located in the Fenway area, and is particularly known for its Engineering, Business and Health Science schools and cooperative education program. Suffolk University, the third largest university in Boston, is located in the Beacon Hill area, and is known for its law school and business school. Boston College, a private Catholic Jesuit university, whose original campus was located in the South End, now straddles the Boston (Brighton)-Newton border, with planned expansions further into Brighton.Boston's only public university is the University of Massachusetts Boston, located on Columbia Point in Dorchester. Roxbury Community College and Bunker Hill Community College are the city's two public community colleges.

Boston has several smaller private colleges and universities. Emmanuel College, Massachusetts College of Art and Design, Massachusetts College of Pharmacy and Health Sciences, Simmons College, Wheelock College, and Wentworth Institute of Technology are founding members of the Colleges of the Fenway and are located adjacent to Northeastern University. New England School of Law, a small private law school located in the theater district, was originally established as America's first all female law school.^[ Emerson College, a small private college with a strong reputation in the fields of performing arts, journalism, writing, and film, is located near Boston Common.

Boston is also home to several conservatories and art schools, including The Art Institute of Boston (Lesley University), Massachusetts College of Art, New England Institute of Art, New England School of Art and Design (Suffolk University), and the New England Conservatory (the oldest independent conservatory in the United States).Other conservatories include the Boston Conservatory, the School of the Museum of Fine Arts and Berklee College of Music.

Several universities located outside Boston have a major presence in the city. Harvard University, the nation's oldest, is located across the Charles River in Cambridge. Its business and medical schools are in Boston, and there are plans for additional expansion into Boston's Allston neighborhood.The Massachusetts Institute of Technology (MIT), which originated in Boston and was long known as "Boston Tech", moved across the river to Cambridge in 1916. Tufts University administers its medical and dental school adjacent to the Tufts Medical Center, a 451-bed academic medical institution that is home to both a full-service hospital for adults and the Floating Hospital for Children. Tufts' main campus, including the renowned Fletcher School of Law and Diplomacy, is located just north of the city in Somerville and Medford.

Boston Public Schools, the oldest public school system in the U.S., enrolls 57,000 students from pre-kindergarten to grade 12.The system operates 145 schools, which includes Boston Latin School (the oldest public school in the United States, established in 1635) which, along with Boston Latin Academy and John D. O'Bryant School of Math & Science, are highly prestigious public exam schools admitting students in the 7th and 9th grades only and serving grades 7–12), English High (the oldest public high school, established 1821), and the Mather School (the oldest public elementary school, established in 1639).In 2002, Forbes Magazine ranked the Boston Public Schools as the best large city school system in the country, with a graduation rate of 82%.In 2005, the student population within the school system was 45.5% Black or African American, 31.2% Hispanic or Latino, 14% White, and 9% Asian, as compared with 24%, 14%, 49%, and 8% respectively for the city as a whole.^.The city also has private, parochial, and charter schools and approximately 3000 students of racial minorities attend participating suburban schools through the Metropolitan Educational Opportunity Council, or METCO.