The Brooklyn Society for the Prevention of Cruelty to Children was granted a charter by the New York State Legislature in 1880 and began operations in January of 1881. Horace B. Claflin, along with several other prominent Brooklynites, established the society to protect children from abandonment, abuse, and child labor. In addition to investigating complaints of cruelty and taking in children in need of housing, the society published circulars aimed at educating the public about laws relevant to child welfare. The society organized placement of children in shelters and foster care, ensured children attended school, and provided medical exams and treatment. Although based in Brooklyn, the society handled complaints and oversaw the placement of children in Queens and Long Island until 1921, when similar societies were founded in Queens County and Nassau County.

For its first 11 years of operation, the society was headquartered at various buildings on Montague Street in Brooklyn Heights. In 1892, the society moved to Schermerhorn Street in the Boerum Hill neighborhood of Brooklyn, establishing a new head office and children's shelter. Over decades of operation, the shelter expanded rapidly and was able to accomodate dozens of children simultaneously. Throughout the early 20th century, the shelter was also used to house delinquent children from Manhattan and Brooklyn.

The society was run on the donations of members, beginning with 253 members in its first year of operation. Endowments and trusts were solicited annually to maintain a steady source of funding. In addition, the society began contracting with the City of New York in the 1970s to work on behalf of the Department of Social Services in Brooklyn. In 1979, the society focused its services on child victims of sexual and physical abuse and began performing social work in addition to providing medical treatment and legal support.

After the society closed the shelter at 105 Schermerhorn in the 1960s, it ran the Warren H. Gunther Group Home in the Bedford-Stuyvesant neighborhood of Brooklyn, along with a short-term group home on Coney Island. The administration of these group homes and care of its residents was the primary focus of the society's efforts from the 1980s into the 21st century. The society closed in 2007.