Tuesday night, the board voted 5-4 to end the policy.
The board majority says that the old policy was unfair and didn't help lower income students succeed. But their plan to help is what their critics say will lead to re-segregation.
"I ask you all to reconsider your position," said Keith Sutton, who is a school board member in the minority.
Before the final vote, another school board member in the minority, Carolyn Morrison, asked her colleague, John Tedesco, tough questions about how they plan to keep Wake County schools diverse in light of the new policy.
"If we deplete the heart of 6,200, what in your opinion will our voluntary desegregation plan look like," Morrison said.
"We had a session on that recently and I've presented what that would look like," Tedesco said.
"I didn't understand it, Mr. Tedesco," Morrison said. "I didn't understand it when I heard it. Can you clarify it?"
But Tedesco simply sat in silence.
Several law enforcement officers were in the board room to keep the crowd under control, a barrier also separated board members from the public. But when the chairman cast the final vote members of the audience burst into protests chanting, "Hey, Hey, Ho, Ho, Segregation has got to go" and "Shame on you."
A sentiment echoed by several school board members who voted against the policy.
"Heartbroken, heartbroken," Morrison said. "It's too many years too many efforts over all this time and we've come so far, we can't go back."
"It may have to be a pill we swallow now, but hopefully the future will be different," Sutton said.
Meanwhile, Tedesco says he's pleased the change is finally official and has a message for his opponents.
"Stop fighting and start working with us," Tedesco said. "If you care about the kids, sit down and talk with us, don't just do your grandstanding for political purposes."
The NAACP has said the new policy will re-segregate schools in Wake County. They are one of several groups that have promised to fight the change.
The NAACP did not show up for Tuesday's vote, but they have been very vocal about its opposition of community schools.
"In North Carolina, there's a lack of policies to insure that local school boards distribute funds equally between high poverty schools and other schools," said Rev. William Barber, NC NAACP president.
Barber says Wake Schools' new student assignment policy violates Brown v. Board of Education -- a landmark decision the Supreme Court made 56 years ago desegregating schools.
The NAACP held a mass meeting on Monday. Rev. Barber said it was the organization's last push to stop Wake's transition to community schools. The NAACP says it's prepared to do whatever it takes to stop the change.