The rally at about 10 p.m. Friday in Union Square was organized in response to the arrests of 22 people who broke into a building on campus and occupied it for five hours earlier in the day.
The second protest ended when police stopped them from marching to Kerrey's house. Police say two protesters were arrested on charges of criminal mischief.
Police were summoned by school officials around 11 a.m. Friday after protesters began occupying the New School building.
Police say the protesters inside the building were arrested peacefully. But outside, protesters clashed with officers and broke through metal barriers.