In colonial New York, young people primarily received education through private schoolmasters and tutors, and free schooling was available to poor families through the Dutch Reformed and Catholic churches. Following the establishment of a state government, the Regents of the University of the State of New York granted charters for secondary schools in the state; the first charter, in 1768, was for Erasmus Hall Academy, located in the present-day Brooklyn neighborhood of Flatbush. Individual school districts in Kings County were created based on village, town, or neighborhood boundaries, with each district receiving funding from local taxes, state contributions, and student tuition. This system continued into the mid-19th century, when Brooklyn created a municipal board of education in 1843 to oversee all schools in the city.

While the number of schools in Brooklyn grew, very few educational opportunities existed beyond the primary grades for the children of poor or working class parents. Secondary schools such as Erasmus Hall and the Brooklyn Female Academy (opened in 1846, and now known as the Packer Collegiate Institute) were private, and therefore only affordable for middle class and wealthy families. The Central Grammar School, founded in 1878, was the first public school in Brooklyn to offer secondary level classes. Out of Central Grammar School, Boys' High School and Girls' High School, the first public high schools in Brooklyn, were formed to meet the demand and need for free public education beyond elementary school. Higher education also became available in Brooklyn around this time, as the Brooklyn Collegiate and Polytechnic Institute (now known as Polytechnic Institute of New York University) conferred its first baccalaureate degrees in 1871, and St. Francis Academy evolved from a monastery and preparatory school to St. Francis College in 1885. Black children in Brooklyn attended separate schools until the 1880s, and the last school in New York City to be explicitly racially segregated was closed in 1900.

New York City consolidated in 1898. Immigration caused the student population to surge and during the 1950s the city's public school system enrolled more than a million students. Residential segregation led to racial segregation in schools and poor outcomes in poor neighborhoods and among students of color. In the 1960s, parents and residents began demanding change, including an especially acrimonious conflict in the Ocean Hill-Brownsville area in 1968. The school decentralization law of 1970 relieved these tensions, assigning governance of elementary and junior high schools to community boards, while high schools remained under the control of the Board of Education. National movements to provide bilingual education and special needs education came to New York City schools in the 1970s, but the city's public schools nonetheless still faced many shortcomings into the 1990s. In 2002, Mayor Michael Bloomberg successfully advocated to have control of the New York City school system transferred to the mayor. In the 2020s, the New York City public school system remains plagued by funding cuts and de facto segregation.