Antisemitism at Columbia University was prevalent in the first half of the 20th century and has resurged in recent years. In the early 21st century, discourse surrounding the Israeli–Palestinian conflict would sometimes lead to accusations of antisemitism, but these individual controversies were typically isolated.

After the October 7, 2023 Hamas-led attack on Israel and the subsequent Israeli invasion of the Gaza Strip, allegations of antisemitism increased acutely as some students and faculty began to organize protests, make statements, and later participate in the campus encampment on Butler Lawn.

In February 2024, Congress opened an investigation into the allegations of widespread antisemitism at Columbia University.

In April 2024, Columbia University President Minouche Shafik condemned antisemitic acts by students and faculty in campus and said the university was in a "moral crisis". United States president Joe Biden and New York City mayor Eric Adams condemned the 2024 anti-Israel protests as antisemitic and condemned the calls for violence and harassment against Jews.

On 14 August 2024, following months of pressure from several prominent members of Congress, President Shafik resigned and was succeeded by Katrina Armstrong as interim President. Later in August, the university's antisemitism task force reported that the university had failed to prevent violence and hate or protect Jews in the university.

In 1920, Columbia University had a 40% Jewish enrollment rate according to Oliver Pollak. Around this time, Columbia imposed quotas on Jewish students in restrict the number of Jews, a practice that quickly expanded to many other prominent American universities.

The process of implementing these quotas began with new requirements to live in on-campus dormitories and new limitations on scholarships. Since a majority of Jewish students in the early 20th century came from impoverished families, many lived at home in order to save money, meaning that this new policy made attending Columbia much more difficult. According to Mark Oppenheimer, Columbia also began to conduct admissions interviews, during which university representatives would detect accents or other signs of Jewish origin for candidates whose surnames were not obviously Jewish. In the years 1920 to 1922, elite Protestant students began to abandon Columbia because of how the campus culture shifted after the number of Jewish students had been halved.

During the 1930s, Columbia rejected both Richard Feynman and Jonas Salk due to their unofficial quotas on Jewish students. Feynman and Salk would instead attend MIT and CCNY respectively.

In 1933, six months after the beginning of Nazi book burnings, President of Columbia Nicholas Murray Butler invited German Ambassador to the United States Hans Luther to speak at the university. Butler rebuked calls from the student body to cancel the speech by claiming that the request to do so would be a surrender to "illiberal theories" and was contrary to academic freedom. Butler also claimed that Luther was entitled to respect from the students of Columbia because he was a representative of "the government of a friendly people".

In June 1936, Butler expelled Robert Burke, President-elect of his class, for his participation in a protest against Columbia's involvement in celebrating the 550th anniversary of Heidelberg University. Burke and other students had been critical of the ceremony because of its close involvement with the Nazi regime and the attendance of Nazi propaganda minister Joseph Goebbels.

The Columbia Unbecoming controversy, which involved disagreements over Israel between Professor Joseph Massad and a number of his Jewish students, began in the early 2000s. Notably, Massad gave a lecture in 2002 titled "Zionism and Jewish Supremacy", which was described in an op-ed by Daphna Berman in the Columbia Daily Spectator. In this op-ed, Berman directly compared the lecture to a swastika that had recently been discovered in a campus bathroom. Throughout this incident and subsequent events, Massad maintained that he was opposed to all forms of antisemitism. The dispute between Jewish students and Massad ultimately culminated in the production and release of Columbia Unbecoming, a film that consisted of taped interviews with students who claimed that their pro-Israel views had led to unfair treatment from Massad in his classes. The production of the film had been supported by The David Project, a pro-Israel college group that later merged with Hillel. Following the formation of an ad-hoc committee by the college to investigate Massad's alleged conduct, it was ultimately concluded in a 24-page report that no evidence existed to support the claims against Massad, and that instead Massad himself had actually been victim to systemic harassment from pro-Israel students and groups. However, the report did acknowledge one confrontation from 2002 that had occurred between Massad and student Deena Shanker during his class "Palestinian and Israeli Politics and Societies".

In late November 2018, psychology Professor Elizabeth Midlarsky discovered antisemitic vandalism in her office. The vandalism included two large red swastikas and antisemitic slurs painted on her wall. Midlarsky had previously been the subject of a similar incident in 2007, when a swastika had been painted on her office door and antisemitic fliers had been placed in her mailbox.

On December 19, 2019, a student at Columbia filed a complaint with the Department of Education, claiming that the administration's inaction had led to an environment where students and staff are "harassed, singled out and discriminated against under the guise of ‘pro-Palestinian’ advocacy." The student claimed that repeated interruptions of pro-Israel events by anti-Israel groups, as well as Israeli Apartheid Week, justified his complaint.

Following the October 7, 2023 Hamas-led attack on Israel, Joseph Massad, a Columbia University professor in Middle Eastern, South Asian and African studies said that the attack on Israel, in which 1200 Israelis were killed including civilians, was a "resistance offensive" and "awesome". President Shafik condemned his comment in April 2024 and said he was under investigation, also saying Massad no longer has a leadership role in the university. InsideHigherEd reported however that in the 2024-24 Academic year Massad chaired an academic review panel in the college of the arts and sciences.

Following the October 7 attack, Mohamed Abdou, a visiting scholar who had said that he sides with Hamas and Islamic Jihad, was hired by the university. In April 2024, president Minouche Shafik said Abdou was on his way out of the university.

Katherine Franke, a professor of law in Columbia, said that all students who have served in the IDF are dangerous and shouldn't be allowed on campus.

The university was sued by Jewish students which said that in the university “mobs of pro-Hamas students and faculty march by the hundreds shouting vile antisemitic slogans, including calls to genocide.”

In a hearing before Congress in April 2024, Columbia University president Minouche Shafik condemned antisemitism and said that "from the river to the sea" is antisemitic. Professors in the university were under investigation according to the president for antisemitic remarks. Shafik said that dozens of students were disciplined and that Columbia University is in a "moral crisis".

During anti-Israel protests, some students called for intifada and urged Hamas brigades to kill Israeli soldiers. Anti-Israel activists sang songs in support of Hamas and chanted slogans expressing solidarity with the organization. The Palestine Solidarity Working Group defended militancy and praised Hamas's attacks against Israel. Anti-Israel protestors also made derogatory remarks towards Jewish students, telling them to "Go back to Europe" and taunting them with calls of "Jews" and "Go back to Poland".

Jewish students reported feeling unsafe, being spat on, and expressed relief at leaving the university. They felt their grievances were not adequately represented by student representatives. One protestor threatened Jewish students, stating, "The 7th of October is going to be every day for you!". Some of the anti-Israel protestors also chanted "From the water to the war (a reference to the Jordan river and the Mediterranean), Palestine is Arab" which is considered a call for the cleansing of the region from Jews and the denial of Jewish rights for self sovereignty in their ancestral homeland.

Journalist Seth Mandel argued that many universities were promoting the idea that Jews should be displaced from their homes because they belong to a race that supposedly belongs elsewhere, citing incidents at Columbia University as an example. The Students for Justice in Palestine (SJP) and the Workers Organizing for Liberation (WOL) both advocated for the destruction of Israel and the targeting of Jewish Israelis, and played a role in organizing the protests at Columbia University.

The President of the United States, Joe Biden condemned the protests saying "Even in recent days, we’ve seen harassment and calls for violence against Jews. This blatant antisemitism is reprehensible and dangerous – and it has absolutely no place on college campuses, or anywhere in our country." The mayor of New York said he was "horrified and disgusted with the antisemitism being spewed at and around the Columbia University campus" and decided to increase police presence around campus. New York State governor Kathy Hochul also condemned the protests, stating that students have the "right to learn in an environment free from harassment or violence". The protestors responded by saying they were peaceful and distanced themselves from non-student protestors.

Following an incident involving Israeli professor Shai Davidai, Robert Kraft, owner of the New England Patriots football team said he would stop donating to the university due to its inability to keep Jewish students safe and was saddened by the hatred growing in campus and the country.

Due to the intensity of anti-Israel protests, Columbia University allowed students to take classes and exams virtually. Rep. Virginia Foxx, chair of the United States House Committee on Education and the Workforce, warned Columbia University that the failure of Columbia to ensure safety was in violation of the university's Title VI obligations, on which is conditioned federal assistance to the university. 

In April 2024, Rabbi Elie Buechler, who is linked to Columbia University's Orthodox Union Jewish Learning Initiative, urged Jewish students to remain home or return home due to safety concerns.

In June 2024, the Jewish Chronicle reported that Columbia academics held classes in protests. The Chronicle also reported that professors questioned Jewish students regarding their opinions on Israel's military campaign. The Chronicle also found that Jewish students were told by the professors that the Jews "control the media", which is a common antisemitic trope.

In July 2024, the university's president and provost announced in a joint statement that three deans had been placed on permanent leave after leaked text messages revealed discussions about Jewish life on campus that "disturbingly touched on ancient antisemitic tropes."

In September 2024, the Columbia Daily Spectator interviewed six Jewish students who were accepted to Columbia for the 2024-2025 school year and declined their offers due to concerns of antisemitism on campus.

On October 14, 2024, Senator Joni Ernst and Representative Elise Stefanik sent a joint letter to Assistant Director in Charge of the FBI's New York Field Office James Dennehy saying that "federal intervention is now necessary" in response to rising antisemitism at Columbia University. The letter was also CC'd to Katrina Armstrong, the Interim President of Columbia University. In the letter, Ernst and Stefanik criticized rhetoric from the Columbia University Apartheid Divest, specifically referencing CUAD's statement that "violence is the only path forward". Shortly after the letter was released, a spokesperson for Columbia said that "calls for violence have no place" at any higher education institution.

A task force on antisemitism was created by the university in late 2023.

The university's antisemitism task force released a report in August 2024 in which it reported on Columbia University's failures to prevent violence and hate or protect Jews in the university. The report called for urgent action against antisemitism. The antisemitism task force reported that antisemitism is common in students' clubs, classrooms and dorms. The antisemitism task force over 20 meetings interviewed 500 students regarding antisemitism in Columbia. According to the report, a Jewish student who placed a mezuza on her dorm's doorway in accordance with Jewish tradition was targeted from October onwards, leading her to leave the dorm. The task force found that a faculty member had recommended prohibiting Israeli military veterans from studying at the university, although Jewish Israelis are required by law to serve in the Israeli military in Israel. Another faculty member told an Israeli student veteran that she had served an "army of murderers". The report also found that a faculty member referred to Jewish donors as "wealthy white capitalists" and accused Jewish donors of laundering money in the university. According to the report, Jewish students were chased off campus, students wearing the Kippah were spat on, and a Jewish woman was pushed. The report found that the term "Zionist" was conflated with Jews and there was a "slippage" that "felt intentional" in the usage of the terms. The report also found that the anti-Zionism in the university is closer to antisemitism than to criticism of Israel. Armstrong, the interim president of Columbia, said the "incidents of antisemitism recounted in this report are completely unacceptable" and said there was "no place" for discrimination or hate in Columbia University.

On September 5, less than a week after the task force's report was published, a group of Jewish faculty from Columbia published an open letter to the university. The letter condemned antisemitism at Columbia while also expressing criticisms of the university's report, which it alleges contains "considerable flaws" and fails to properly define a number of terms that were pertinent to the report's main goals. In particular, it asserted that Columbia's task force had exaggerated the number of antisemitic incidents reported by Jewish students by improperly conflating "discussions or chants that made some Jewish students feel uncomfortable" with antisemitism. On September 17, thirty-four Jewish faculty members jointly published an op-ed in the Columbia Spectator that criticized the Spectator's coverage of the aforementioned open letter, especially its quotes of statements by Professors Nicholas Lemann and Ester Fuchs (both co-chairs of the task force) that they said "wilfully mischaracterized" views of the writers and positions taken in the open letter.

• Antisemitism in US Higher Education