It comes after pro-Palestinian protesters set up an encampment on Penn's campus for weeks.
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Some schools, like Columbia University and the University of Southern California, canceled their ceremonies because of similar protests.
"The whole campus, the whole senior class, was very scared but super grateful to have a graduation," said Penn graduate Adrien Chevrier. "A moment of a lot of division, a lot of tension on campus, but it was great to be together at a ceremony and I think it really brought the campus together."
The ceremony went off without any issues or disruptions, although some students still made a silent statement through their clothing.
One student waved the Palestinian headscarf, others were seen with 'Free Palestine' written on their graduation caps.
RELATED: Protesters gather at Drexel University campus, set up new encampment
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"It's been a hard year for the world and for Penn," spoke the University's interim president, J. Larry Jameson.
Students, staff, and parents were all required to go through airport-style security to enter the ceremony.
Large bags, flags, and posters were all prohibited.
"Because of COVID, I was like, not again. But I'm really glad Penn pushed through and was able to get it together. It's been a joyful event. Safe. Everyone is happy," said Penn graduate Dangela Fonseca. "I'm just so proud to be here. I'm happy. My mom's with me. It's one of the best days of my life."
Roughly 6,000 graduates took part in the ceremony. Thiswas theuniversity's268th commencement.
Siddhartha Mukherjee, a physician and author, provided the commencement speech.
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According to the university, several students who participated in the encampment at Penn earlier this month may not receive their diplomas.
School leaders told Action News that three graduating seniors had their cases expedited through the Office of Community Standards and Accountability.
They were unable to participate in graduation ceremonies due to not responding to the letters to resolve their cases.
On Friday night, 19 protesters, seven of whom were Penn students, were arrested during a demonstration on campus.
Roughly 24 hours later, about 40 to 60 pro-Palestinian protesters set up another encampment on Drexel University's campus.
Drexel's graduation ceremony is expected to take place sometime in June.