Protest organizers at Jones College Prep planned the demonstration for 1:45 p.m. inside the school's lobby.
Paper went up to shield the lobby's windows, and Chicago police bike officers stood by as dozens participated in what they called a peaceful demonstration.
"We wanted to show our support to growing encampments around the country, including Northwestern, Columbia and general protest for Palestinian genocide," protest organizer Atticus said.
While most Jones students did not participate and went to class, some supported the protesters' right to demonstrate
"I feel everybody should be able to express themselves, whichever way they want ... and I think it is good the school is giving the opportunity to do that," student Oliver Minkov said.
The sit-in was opposed by several Jewish students.
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They feared the protest would incite antisemitism based on a previous Jones student walk-out and college campus demonstrations.
"When I see all of this anti-Zionism, it really feels like antisemitism," student Max Rubenstein said.
Student Mira Rosenblum said she and her peers headed into school Wednesday somewhat on-edge ahead of the sit-in.
"A lot of the speakers are also seniors and so I see them in class and I have to walk around school getting dirty looks for what I support," Rosenblum said.
But pro-Palestinian student organizers deny their message is antisemitic.
"Anyone who is antisemitic and calls themselves pro-Palestinian is not pro-Palestinian," Atticus said.
Jewish organizations are calling on schools to provide all students with more education on the history of the centuries-old conflict.
"If the students feel so passionate about this, we should be educating them on productive- and peaceful-oriented models for dialogue," said Sarah Van Loon, with the American Jewish Committee.
The few students who walked out of school after the protest, got on a bus and headed south to join demonstrators at Kenwood Academy and University of Chicago.
Protest organizers could be seen passing out fliers before school Wednesday morning and posting the documents to nearby light poles, trying to spread word about the gathering.
ABC7 tried to speak with the students organizing the demonstration, but they declined to comment.
"At least all the Jewish students are a little uneasy when they see this large scale protest," Rubenstein said.
Freshman Rubenstein said he planned to be at a counter-protest Wednesday inside the school with other Jewish students holding an Israeli flag.
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He and others passed out gold ribbons before class to represent Israeli hostages taken by Hamas.
Chicago Public Schools issued a statement on the demonstration, writing in part, "While we support students' constitutional right to free expression, harassment, discrimination, and bias-based harm have no place in our school community and will not be tolerated."
CPS policy limited the demonstration to 30 minutes. The principal said those late to class after the demonstration would receive an unexcused absence.
The College Decision Day Celebration postponed because of the protest was rescheduled for Friday.