At Harvard University, the rabbi at a menorah lighting ceremony was unusually blunt.

“It pains me to have to say, sadly, that Jew hate and antisemitism is thriving on this campus,” Rabbi Hirschy Zarchi of Harvard Chabad said on Wednesday.

“Twenty-six years I’ve given my life to this community,” he said. “I’ve never felt so alone.”

Just the night before, he told the gathering, a woman passing by the Hanukkah candle-lighting ceremony yelled that the Holocaust was fake. When Harvard Chabad hosted a screening of an Israeli military film with footage from the Oct. 7 Hamas attacks, he said the campus police advised him to get security for his family. Even the giant menorah, prominently displayed in Harvard Yard, was packed away each night, he said, as in past years to protect it from vandalism.

Claudine Gay, Harvard’s president, stood nearby, waiting to light a candle. As the rabbi spoke, she stared straight ahead, looking stricken.

The uproar over Dr. Gay’s congressional testimony — on whether students would be punished if they called for the genocide of Jews — has exposed the deep anxiety, anger and alienation of many of Harvard’s Jewish students, alumni and faith leaders.

In interviews, many Jewish members of the Harvard community described their growing estrangement from campus. Protesters have disrupted lectures, shouting through bullhorns that the war in Gaza was a genocide. Antisemitic messages have been posted on social media. Some students have decided to check their Zionist beliefs in the classroom and in the residence hall. A few have traded in their kippas, or skullcaps, for baseball hats.

For students who are feeling increasingly isolated, it did not help that many of their Jewish peers had joined the pro-Palestinian demonstrations.

The fall semester closed with more tension. The Harvard Corporation, the school’s governing board, deliberated for hours on Monday before deciding to resist calls to force Dr. Gay’s resignation.

The previous day, as students prepared for final exams, pro-Palestinian student groups staged a large, silent demonstration at Widener Library, occupying a reading room. Rows of protesters, many wearing kaffiyehs, the Palestinian scarf, sat at tables with open laptops, all displaying the same flier: “No Normalcy During Genocide. Justice for Palestine.”

After one of the most trying weeks in the university’s recent history, and as the campus emptied out for the holidays, some Jews in the Harvard community called for Dr. Gay and the university to reset for the new year. Something needs to be done, urgently, they said, to fix the perception that the institution had turned its back on Jews.

The issue is about more than the Israel-Hamas war. Jews, who have had high admittance rates in the Ivy League, are declining in numbers. At Harvard, the decline has been especially pronounced, falling to less than 10 percent of the student body today from roughly 20 percent a generation ago, according to estimates by outside scholars and surveys of the student body, including one conducted by The Harvard Crimson, the student newspaper.

Those figures reminded some alumni of the university’s history of bias against Jewish applicants. In the 1920s, Harvard’s Jewish population accounted for about a quarter of the student body. But then the school instituted quotas aimed at limiting their admission, which lasted for decades. The percentage of Jewish students dropped to roughly 10 to 15 percent of all students, according to Marcia Graham Synnott, whose book “The Half-Opened Door” examined discrimination in the Ivy League.

That legacy helped feed the unease over the current campus politics.

“To see newly resurgent antisemitism against this backdrop of fairly recent, wonderful acceptance is a very, very painful thing for a lot of Jews,” said Mark Oppenheimer, a journalist who has studied the Jewish experience in the Ivy League. “We thought that these were institutions that were profoundly welcoming and were going to stay profoundly welcoming.”

Dr. Gay’s critics said she was slow to condemn the Hamas attacks. Nor had she, in their view, been quick enough to speak out against the pro-Palestinian student groups who said they held Israel “entirely responsible for all unfolding violence” in the conflict.

In response, a Harvard spokesman on Saturday pointed to a half-dozen events on campus where Dr. Gay had joined Jewish students since Oct. 7, and he referred to her earlier statement announcing the creation of an advisory group on antisemitism. The group, Dr. Gay said, would aim to “intervene to disrupt and dismantle this ideology.”

Trust almost completely broke down after the Dec. 5 congressional hearing, when Dr. Gay; Sally Kornbluth, M.I.T.’s president; and Elizabeth Magill, of the University of Pennsylvania, appeared to dodge questions on disciplining students if they called for the genocide of Jews. Ms. Magill resigned as president four days later.

Dr. Gay apologized for her testimony. “When words amplify distress and pain, I don’t know how you could feel anything but regret,” she told The Harvard Crimson.

She still must lead a deeply divided campus and continue to try to balance the freedom to protest with the fears of many Jews, who say certain slogans used by pro-Palestinian demonstrators — like “from the river to the sea” and “globalize the intifada” — are antisemitic and a call for violence against them.

But Ari Kohn, 20, a Jewish sophomore from Toronto, said that while she “believes in the state of Israel,” she has not experienced the pro-Palestinian movement at Harvard as threatening.

“It’s important to understand when people call for intifada to ask them, ‘What do they mean by that?’” she said. “We’re all using different definitions of the same word. Giving the benefit of the doubt to my peers, my faculty and my community is really important.”

To other students, the campus has become an alien place.

“After Oct. 7, there was a very palpable, tangible shift,” said Shabbos Kestenbaum, an orthodox Jew and graduate student at Harvard Divinity School.

He said his classmates — “who I quite literally sit next to” — have published messages on their social media “that explicitly praise Hamas, that deny the rape and abduction of Israeli women.”

He added, “I’m certainly not comfortable, and I wouldn’t even say welcomed, in many spaces around campus.”

As criticism rose, Dr. Gay announced the advisory group to combat antisemitism.

There has already been a defection. After Dr. Gay’s congressional testimony, Rabbi David Wolpe, a visiting scholar at Harvard Divinity School, resigned from the committee.

In an interview after the Harvard Corporation announced its support for Dr. Gay, he said that he found her to be “smart, thoughtful, genuinely curious.” But he said that he quit because antisemitism at Harvard was growing worse and he was not convinced the committee would make a difference.

“I remain hopeful — but unconvinced — that Harvard will change in the ways that I wish it would,” he added.

In a response to his resignation, Dr. Gay said she was “committed to ensuring no member of our Jewish community faces this hate in any form.”

Some have resisted the description of a campus rife with antisemitism.

Noah Feldman, a legal scholar and director of a program on Jewish and Israeli law, said he had “never once” experienced antisemitism on Harvard’s campus, even during the years when as an observant Jew, he regularly wore a kippa.

How to move ahead in such a stalemate? Rabbi Getzel Davis of the Harvard Hillel chapter said there were practical things to be done.

He noted that until recent changes instituted by Dr. Gay, the university’s various diversity programs had not made Jews a focus of their work.

But now students reporting bias incidents are having trouble navigating Harvard’s diversity, equity and inclusion bureaucracy — so much so that Hillel hired a part-time staff member to assist with the process.

Rabbi Davis said the university should do a better job enforcing its rules against hateful speech and actions. He would like to see more events for interfaith reflection and sharing. And he said the university should educate students about the history of antisemitism.

That might help some students.

Maya Bodnick, 19, a Harvard sophomore from Atherton, Calif., said that she was cautious about sharing her liberal Zionist views on campus, because many on the left were simply not open to her perspective. Many of these students, she said, categorized Jews as oppressors, without acknowledging their suffering at the hands of others for millenniums.

“It has been very disappointing,” she said. “I worry that my peers have a very skewed understanding of Judaism and antisemitism.”