WASHINGTON — The national board of the N.A.A.C.P. voted Friday to dismiss the organization’s president, Cornell William Brooks, after only three years, pledging a “systemwide refresh” at the nation’s largest and most storied civil rights group in order to confront President Trump more vigorously.

Mr. Brooks, who said in an interview that he was “baffled” and saddened by the decision, will leave the organization at the end of June when his contract expires. The group will search for a new leader while Leon W. Russell, the chairman of the board, and Derrick Johnson, the vice chairman, head up day-to-day operations.

The sudden change at the top of the N.A.A.C.P. shows how the energy of liberal activists in the era of President Trump is forcing upheaval even in institutions like a century-old civil rights stalwart. Mr. Brooks was hardly reserved in his own activism. He was arrested in January for leading a sit-in at the Alabama office of Senator Jeff Sessions, trying to block his confirmation as attorney general.

But the board of the N.A.A.C.P. wants a new face of the organization. Mr. Russell and Mr. Johnson said the group needed to more effectively push back against Mr. Trump’s stances on issues like voting rights laws, public education, environmental policy and the criminal justice system. The group, which has been eclipsed in many ways by the more youthful Black Lives Matter movement and the broader opposition to Mr. Trump, is embarking on a listening tour of cities across the nation to get ideas about how it can remain relevant.