The student arm of the civil rights movement, led by SNCC (the Student Nonviolent Coordinating Committee, founded in 1960 at a conference of 120 black student activists in North Carolina), focused on fighting segregation through mass action and local, community-based activity. The SNCC organizational structure was made up of a non-hierarchical Coordinating Committee and groups of fieldworkers who worked with local African American communities and determined their own direction in response to the local needs. SNCC used this model of grassroots, community organizing to make change in the daily lives of ordinary people – in contrast, they argued, to the slow pace of federal change and its lack of impact on most regular folks. SNCC's approach was more radical than that of the national black organizations and the African American elite, who sought change through cooperation with whites in positions of power and through the legislative and judicial systems. SNCC, in contrast, operated through direct confrontation, grassroots organizing, and civil disobedience.

In 1964, The Council of Federated Organizations (COFO), with heavy student leadership from SNCC, launched the Freedom Summer project, a new campaign that built on and expanded the community organizing that SNCC had been doing for a few years in the South. Freedom Summer brought about 1,000 northern students – mostly white, mostly relatively affluent – to Mississippi to register voters, help organize the Mississippi Freedom Democratic Party (MFDP) as an alternative to the state's all-white Democratic Party, and run Freedom Schools and community centers for local African American communities. Approximately half of the white Freedom Summer volunteers were Jewish.

Freedom Summer targeted Mississippi because it was the poorest state in the US and the one least changed by civil rights activism. In 1964, 42% of the state's population was African American, but less than 5% could register to vote due to literacy tests, poll taxes, and physical intimidation. The racial caste system was held firmly in place by a tradition of violence against African Americans.

The point of bringing white students to Mississippi was, in part, to take strategic advantage of America's racism. The organizers guessed that violence against white northern college students would attract the attention of the government and the nation, whereas regular violence against African Americans did not. The federal government would then be forced to protect the civil rights workers and stand up to state authorities.

Sadly, this guess was proven correct immediately, when three civil rights workers – James Chaney (21 years old), an African American from Mississippi, and Michael Schwerner (24) and Andrew Goodman (20), both Jews from New York – went missing on their first day in Mississippi in June while investigating the burning of a black church. (Michael Schwerner, with his wife, Rita, had actually spent the previous six months organizing in Mississppi with CORE and had just returned to the South with the first cohort of Freedom Summer volunteers). The bodies of the three men – beaten, shot, and buried in a dam – were found six weeks later. (The search had also uncovered the bodies of seven black men whose disappearance had not garnered any national attention.) Mississippi officials refused to prosecute the suspected killers for murder, so the US Department of Justice brought a case against 18 men, including the Sheriff Laurence Rainey and Deputy Sheriff Cecil Price, on the charge of depriving the three men of their civil rights (by killing them). Seven men were found guilty but served relatively short sentences. Edgar Ray Killen, who had planned and directed the murders, was acquitted in the 1967 case but was finally convicted of three counts of manslaughter in 2005.

Over the course of Freedom Summer at least three other civil rights workers were murdered and volunteers also experienced 1,000 arrests, 80 beatings, 35 shooting incidents, and 30 bombings of homes, churches, and schools.

In addition to the daily intimidation and fears of violence, Freedom Summer volunteers also experienced interpersonal tensions. White volunteers – many of whom had never before had direct contact with African American communities – were not always aware of their own privilege, sense of entitlement, and in some cases, ingrained racist assumptions. Some white activists found the cultural differences they encountered surprisingly challenging and had trouble communicating with local African Americans in the communities in which they worked. With the volunteers working together so many hours each day and often living in close quarters, sexual relationships inevitably developed, and these relationships brought out further racial tensions – especially among black men and white women, who sometimes felt as if they were being used by the other to prove either sexual prowess or their racial politics, and black women and white women, who sometimes competed over the attention of black men. These relationships were further intensified by the danger of white women and black men working together; the mere fact of a white woman in the company of a black man could get one or both of them killed. Tensions around gender roles also arose, as some women wondered why, in a movement committed to equality, they were so often relegated to the housekeeping and administrative tasks and excluded from leadership roles.

But the intensity of the experience also created a powerful sense of purpose and community, an embodiment of the ideal of the "beloved community" of blacks and whites working together for a common cause. Many Freedom Summer volunteers recall their time in the South as the most powerful and transformative experience of their lives. Their eyes were opened to a "different America," as one volunteer put it, and while often a painful realization, it changed their worldview and their definition of community.

This communal spirit was heightened by certain practices such as the singing of "freedom songs" – traditional Negro spirituals or folk songs about the struggle for freedom and redemption that took on new meaning in the cauldron of the civil rights struggle. Meetings often began and ended with the singing of freedom songs; freedom songs also helped boost spirits and strengthen resolve in jail and during other stressful times, and helped activists remain peaceful when faced with violence.

Because Freedom Summer volunteers were predominantly young students, the project sparked some generational tensions. Many of the volunteers' parents, even if they supported the civil rights movement in general, were concerned about the violence that their children faced and discouraged them from participating. Some parents disagreed with the radical tactics of the project, believing that more traditional routes to change – legislative, judicial, etc. – should remain the focus of the civil rights movement. Others were inspired by their children's commitment to civil rights and even learned from them. The letters volunteers wrote home testify to the varied responses of concern and incomprehension, disapproval and pride that they faced from family.

The Freedom Summer project succeeded in its goal of attracting national attention to Mississippi and gaining sympathy from northern liberals. The project created more than 40 freedom schools (some of which became enduring, community-based institutions) that taught reading, math, politics, and African American history to black children. Over the course of the summer about 60,000 African Americans signed up to join the MFDP, and the newly-formed party sent a slate of delegates to the August 1964 Democratic National Convention, demanding to be seated in place of the all-white regular state delegation.

At the convention in Atlantic City, however, the MFDP ran into opposition from President Johnson, who did not want to alienate southern Democrats. MFDP leaders made a strong case for the party, with delegates such as local activist Fannie Lou Hamer testifying before the convention about the racism and brutality that blacks faced daily in Mississippi. Ultimately, Johnson offered a compromise to give MFDP two token seats, but the MFDP delegates rejected the offer, arguing that they had come to challenge the validity of the all-white Mississippi delegation, not to take two symbolic seats beside it. The defeat of the MFDP intensified the disillusionment of student activists with the Democratic Party and the political establishment.