Pence accepted an invitation instead.
The plan is for fifty to one hundred students to get up and quietly leave the commencement as soon as Pence starts to speak.
And he called on the graduates to keep President Donald Trump in mind as they plan for their future and prepare for the obstacles that might threaten it. "Dreams may be deferred but they must never be abandoned".
Pence encouraged the graduates to be strong and never fear criticism.
Senior Grace Watkins explained to CBS News that the students will walk in as normal and then walk out when the time comes for Pence to speak. "We also will walk out in dignity and solidarity with all marginalized people affected by Pence's politics, both on this campus and throughout our nation".
Pence will become the first vice president to deliver a commencement speech at Notre Dame when he receives an honorary degree on Sunday, according to the university.
Local groups will also protest Pence's speech, but will do so off campus.
Former student body president and one of the protest leaders Bryan Richetts said, "The flag drop was round one". They believe that the politics Pence, the former IN governor who was raised Catholic, represented contradicted the Catholic social virtues Notre Dame extols.More news: Harden, James top All-NBA team; George, Hayward shut out
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Ricketts also said the university administration has not resisted their protest.
The university's vice president for public affairs and communications, Paul Browne, told the Indianapolis Star, the school would only intervene "if the ceremony was seriously disrupted or anyone's safety was put at risk".
WGN-TV reported that Notre Dame President Reverend John I. Jenkins called it "fitting" that on the school's 175th anniversary of its founding, that a "native son" will be recognized.
A professor at Indiana University-South Bend, Lidinsky rejects Pence's views on women's health and reproductive health, including his commitment to defund Planned Parenthood and his strict stance on abortion, which "counters sound medical decisions that women make with their doctors".
When Pence stepped to the lectern, he received a standing ovation.
"Even those who disagree with Mike Pence recognize him as a man of principle".
"I want to assure you, President Donald TrumpDonald TrumpTrump's 2018 budget would slash EPA spending by 30 percent: report Are American airports really "third-world" in quality? It went pretty well", said Carolyn Steglich, a member of the Slippery Rock Huddle, which organized the event.