In the early 1890s, another building, the Brooklyn Institute of Arts and Sciences, was built with the purpose of becoming a general, all-purpose museum. One of the institute's curators suggested that a new children's museum be constructed in a nearby house that the museum bought to store its scientific collections and library books. The Institute also allowed the public to use the collections and books to conduct research.
The new children's museum opened at the house in December 1899. A few years later, Anna Billings Gallup was appointed curator and later became the director until she retired in 1937. Over the next several decades, the museum's reputation grew. By 1940, approximately 9 million people had visited the museum. In 1977, the museum moved into a new building which was later renovated in 1995. The museum underwent another renovation between 2002 and 2008.