Motley died of congestive heart failure at NYU Downtown Hospital on Wednesday morning, according to her son, Joel Motley III.
Motley's early career found her fighting racism in many of the nation's landmark segregation cases. After a brief foray into politics, in 1966 she became the first black woman appointed to the federal bench and began a distinguished four-decade span as a judge.
"She's going to be missed," said Chief Judge Michael Mukasey in U.S. District Court in Manhattan, where Motley served. "She is a person of a kind and stature the likes of which they're not making anymore."
Motley was born in New Haven, Conn., the ninth of 12 children. Her mother, Rachel Baker, was a founder of the New Haven NAACP. Her father, Willoughby Alva Baker, worked as a chef for student organizations at Yale University.
Her interest in civil rights grew after she was turned away at age 15 from a public beach because she was black.
"Judge Motley had the strength of a self-made star," federal Judge Kimba Wood said. "As she grew, she was unfailingly optimistic and positive - she never let herself be diverted from her goal of achieving civil rights, even though, as she developed as a lawyer, she faced almost constant condescension from our profession due to her being an African-American woman."
Motley earned a degree in economics in 1943 from New York University, and three years later, got her law degree from Columbia Law School.
In 1945, she became a law clerk to Thurgood Marshall, who was then chief counsel of the NAACP's Legal Defense and Educational Fund. Over the next two decades, she rose to associate counsel of the organization and worked on some of the nation's most famous civil rights cases, including preparing the draft complaint in 1950 for what would become Brown v. Board of Education.
In her autobiography, "Equal Justice Under Law," Motley said defeat never entered her mind. "We all believed that our time had come and that we had to go forward."
The Supreme Court ruled in her and her colleagues' favor in May 1954 in a decision credited with toppling public school segregation in America. The ruling, though, touched off resistance across the country and led to some of the racial clashes of the 1960s and more litigation.
At the heart of much of it was Motley, from a case in Little Rock, Ark., in 1957 that led President Eisenhower to call in federal troops to protect nine black high school students to leading the legal charge to win James Meredith's entry into the University of Mississippi in 1962.
Also in the early 1960s, she successfully argued for 1,000 school children to be reinstated in Birmingham, Ala., after the local school board had expelled them for demonstrating. She represented so-called "Freedom Riders" who rode buses to test the Supreme Court's 1960 ruling prohibiting segregation in interstate transportation. During this time, she represented King as well, defending his right to march in Birmingham and Albany, Ga.
From 1961 to 1964, Motley won nine of 10 civil rights cases she argued before the Supreme Court.
In the late 1950s, Motley took an interest in politics and by 1964 had left the NAACP and become the first black woman to serve in the New York State Senate.
In 1965, she became the first woman president of the borough of Manhattan, where she worked to promote integration in public schools.
In 1966, President Johnson nominated her to the federal bench in Manhattan. She was confirmed nine months later, though her appointment was opposed by conservative federal judges and southern politicians.
Over the next four decades, Motley handled a number of civil rights cases, including her decision in 1978 allowing a female reporter to be admitted to the New York Yankees' locker room.
Motley is survived by her husband and son, three sisters and brother.