The value of a college degree is in doubt, facts are under siege, and campus endowments are being chipped away, Harvard president Drew Faust said Thursday — but she used her final commencement speech to vigorously defend higher education.

Colleges and universities are “beacons of hope,’’ Faust said.

“These past 11 years have only strengthened my faith in higher education and its possibilities. In their very essence universities are about hope and about the future, and that is at the heart of what we celebrate today.’’

Faust steps down from her term as Harvard’s first female leader in its 381-year history in June.

Under her leadership, Harvard has gone through its share of triumphs and challenges, Faust said.

The economy collapsed and recovered. The university lost nearly one-third of the value of its $38 billion endowment during the financial crisis, triggering layoffs and wide-ranging reforms of its wealth-management practices.

Harvard was embroiled in a student cheating scandal and a secret search of employee e-mails.

There have been sexual assault and sexual harassment crises, and a slew of social movements, from Occupy Wall Street to Black Lives Matter to #MeToo.

“There has, indeed, been a good measure of chastening,’’ she said.

Faust, who has often seemed reticent about being in the spotlight, on Thursday embraced the attention.

She stomped her feet to “Harvardiana,’’ the university’s fight song, even shouting “Radcliffe!’’ in between the official lines of “Harvard!’’ — a reference to the former women’s college that officially joined with the university just before she became its dean in 2001.

Faust even dropped a reference to rock guitarist Jimi Hendrix’s debut album, “Are You Experienced.’’

“I would have to answer affirmatively,’’ Faust said.

Yet Faust acknowledged there is still work to do and urged students and faculty to tackle the difficult problems facing society and the university, from climate change to free speech.

“We must be a place where facts matter, where reasoned and respectful discourse and debate serve as arbiters of truth,’’ she said.

“Protecting and nourishing free speech is for us a fundamental commitment, and one that demands constant attention and vigilance, especially in a time of sharp political and social polarization.’’

Lawrence S. Bacow, the former president of Tufts University, is set to step into Harvard’s top job on July 1.

Civil rights leader and longtime congressman John Lewis, the headline speaker for the commencement ceremony, thanked Faust for getting into “good trouble’’ by using the university’s influence to encourage greater student diversity and inclusion.

Lewis, a Georgia Democrat who helped organize the 1963 March on Washington and was repeatedly jailed for his civil rights activism, urged students to similarly speak out when they see injustice.

“You’re never too young to lead; you’re never too old to lead. We need your leadership now, more than ever before,’’ Lewis told the graduates. “You cannot afford to stay on the sidelines.’’

Lewis, who was also the featured speaker at Boston University’s commencement on Sunday, repeated similar themes at Harvard.

He marveled at how the country has changed since his childhood in a segregated Alabama.

Some years ago, a former Klu Klux Klan member who had beaten him during a protest at a bus station in 1961 in Rock Hill, S.C., came to his office and asked for forgiveness, Lewis said.

“We need to create a society where we can reconcile,’’ Lewis said.

“We all live in the same house; we must all hold that house down.’’

Deirdre Fernandes can be reached at deirdre.fernandes@globe.com. Follow her on Twitter @fernandesglobe.