Baker joined the Young Negroes Cooperative League and in 1931 was appointed its national director. She was also employed by the Works Progress Administration to provide literacy and consumer education to workers.
In 1940 Baker became a field secretary of the National Association for the Advancement of Coloured People (NAACP) where she was involved in the anti-lynching campaign. Over the next few years Baker attempted to persuade the organization to become involved in community-based activism. Baker also played a leading role in the campaign to desegregate New York City public schools. According to Susan Gushee O'Malley: "her strength was to evoke in people a feeling of common need and the belief that people together can change the conditions under which they live.
In 1956 Baker and Bayard Rustin established Friendship, an organization dedicated to raising money for the fight against Jim Crow Laws in the Deep South. The following year she moved to Atlanta to work with Martin Luther King and the Southern Christian Leadership Conference (SCLC). While in Atlanta she also ran the Crusade for Citizenship, a voter registration campaign. Baker disagreed with the SCLC's policy of having a strong central leadership. Baker, who favoured local, grassroots action, left the organization in 1959.
In February 1960, Greensboro, North Carolina, a small group of black students started a student sit-in at the restaurant of their local Woolworth's store which had a policy of not serving black people. In the days that followed they were joined by other black students until they occupied all the seats in the restaurant. The students were often physically assaulted, but following the teachings of Martin Luther King they did not hit back.
Baker became involved in this campaign and in October, 1960, helped to establish the Student Nonviolent Coordinating Committee (SNCC). Baker commented: "The Student Leadership Conference made it crystal clear that current sit-ins and other demonstrations are concerned with something much bigger than a hamburger or even a giant-sized Coke. Whatever may be the difference in approach to their goal, the Negro and white students, North and South, are seeking to rid America of the scourge of racial segregation and discrimination - not only at lunch counters, but in every aspect of life."
SNCC adopted the Gandhian theory of nonviolent direct action. This included participation in the Freedom Rides during 1961. Leading figures in the organization included Robert Moses, Marion Barry, James Lawson, Charles McDew, James Forman and John Lewis. According to Susan Gushee O'Malley: "In the following years, Baker was the older person behind SNCC students who listened, counseled, advised, and nurtured the civil rights workers who organized the freedom rides, worked in voter registration, and broke segregation in the South."
In 1964 Baker returned to New York City and remained active in the civil rights movement. She was also a supporter of freedom struggles in Africa, a national board member of the Puerto Rican Solidarity Committee and vice-chairperson of the Mass Party Organizing Committee.
Ella Josephine Baker died on 13th December 1986.