• Harvard President Claudine Gay's resignation was just the latest upheaval at one of the nation's top colleges.
• For college applicants, the move adds more uncertainty to an admissions process that was already in flux.
• Early applications ahead of the Nov. 1 deadline sank 17%.

Harvard University President Claudine Gay's resignation Tuesday is just the latest upheaval at one of the nation's top colleges.

For college applicants, the move adds more uncertainty to an admissions process that was already shifting in the wake of the Supreme Court's ruling against affirmative action.

"I don't expect Harvard to lose its crown as one of the most coveted universities," said Hafeez Lakhani, founder and president of Lakhani Coaching in New York. However, "I've seen students really shaken to the core."

Harvard early admission applications fall 17%

This year's early admissions cycle, which marked the first in which race was not considered, reflected a changing dynamic.

Early applications ahead of the Nov. 1 deadline — amid multiple incidents of antisemitism on campus following the Oct. 7 attack on Israel by Palestinian militant group Hamas — sank 17%. There were 7,921 early applicants to the Class of 2028, down from 9,553 last year, the Harvard Crimson reported.

Harvard admitted 8.74% of the total pool, an increase of more than 1 percentage point from last year's 7.56%, notching the highest early action acceptance rate since 2019.

More from Personal Finance:
Is an Ivy League degree worth it?
New FAFSA ‘soft launch’ hits snags
Fewer students are enrolling in college

"Whatever change we see this year, in time, that will probably normalize," Lakhani predicted.

Indeed, a slightly more favorable acceptance rate could have already prompted more students to apply by the regular decision deadline on Jan. 1, according to Christopher Rim, president and CEO of college consulting firm Command Education.

Gay's resignation, which came shortly after that deadline and roughly one month after Gay and then-University of Pennsylvania President Liz Magill were criticized for answers they gave at a congressional hearing on campus antisemitism, could also cause more students to apply next year, he added.

"This is the first time I've ever seen something like this," Rim said. "The brand took a huge hit, but I think it's going to recover ultimately."

Harvard did not immediately respond to CNBC's request for comment.

In response to Gay's resignation, Alan Garber, Harvard's provost and chief academic officer, who will now serve as the university's interim president, said in a statement, "I am confident we will overcome challenges we face and build a brighter future for Harvard."

However, future applicants are increasingly motivated by social justice-related considerations, Lakhani said, and that will continue to drive their decisions about college. "There's a very sensitive narrative happening," he said.

"In the short term, it's a Harvard and Penn problem; in the long term it is a higher education problem," he said.

Don't miss these stories from CNBC PRO:

• These stocks will be the biggest S&P 500 winners of 2024, according to analysts
• Here's where to invest $50,000 in the new year, according to the pros
• Could a bitcoin ETF approval be a sell-the-news event? Here's what to expect if it happens
• These stocks will be the biggest Dow winners of 2024, according to analysts
• Oprah's flip on weight loss drugs is a sign of what's to come for the 'Ozempic trade' in 2024

Subscribe to CNBC on YouTube.