In a stunning turn, the Board of Education refused to accept Willis’ resignation, bolstering his position as the ruler of Chicago’s education system. This refusal was also a stinging rebuke of the protests against Willis’ reign, and warranted swift action by protestors. This was the final sign to the citizens' groups that they had no support from city institutions, and the only option left to them was drastic, direct action. It was here that the idea for a citywide boycott was born.

The boycott was the product of careful organization, planning, and strategic thinking. Many groups came together to form the Coordinating Council of Community Organizations (CCCO), who worked with other already-established activist groups, such as the Congress for Racial Equality (CORE) and Student Non-Violent Coordinating Committee (SNCC), both of whom had been active in the struggle against the more overt segregation of the Jim Crow south. After several meetings, CCCO declared the boycott was to take place on October 22, 1963. Students were encouraged to skip school that day and to march towards CPS headquarters in downtown Chicago.

Participants in the march — about 10,000 of the nearly 225,000 who left school for the day — were trained to stay calm during the demonstration, even in the event of mass arrests or police violence. Just as the beginnings of the protest were in solidarity with those fighting for freedom in the southern states, so too did this event draw from the experience and expertise of those who had participated in those struggles directly.

While some students chose to march, many — especially younger children— attended Freedom Schools. These were classes organized by parents and activists to continue their education during the pause in official activity. These were inspired by similar efforts in states like Virginia and Mississippi, where Freedom Schools were set up to educate Black children whose educational progress was deliberately sabotaged by inadequate public schools. In addition to the typical curriculum of reading and math, the Freedom Schools taught the basics of general civic participation, black history, and encouraged their students to question the assumptions of the society they found themselves in.

The first boycott received a great deal of attention in the press, and is now regarded as one of the preeminent Civil Rights actions to occur in the northern states. Inspired by this, a similar strike would occur among students in New York City and many other cities. Movements like these were integral to revealing segregation as a national American problem, and not one that was only for "backwards" southern states.