Brown University’s president said Monday that she would step down at the end of the coming academic year, after steering Brown through fraught negotiations with the Trump administration and the agony of a campus shooting that left two students dead.

The president, Christina H. Paxson, has been in her post longer than any other current leader of an Ivy League university. She became president in 2012.

In an open letter on Monday, she described her resignation as “the right decision for me and my family” and noted that she had previously extended her tenure to manage the university’s clash with the federal government.

The university extinguished some of that fight last summer, when it agreed to a settlement that included Brown’s $50 million commitment to work force development programs in Rhode Island. Brown forged the agreement after the Trump administration moved to block $510 million in research funds, which was part of a broader campaign to punish elite universities for perceived antisemitism and inaction over protests against the war in Gaza.

Although the Brown agreement explicitly preserved the university’s authority over academic matters and restored the research money, its terms also aligned the school with the administration’s approaches to transgender athletes and “merit-based” admissions policies.

Dr. Paxson faced substantial campus criticism over the settlement, which some regarded as an act of capitulation to an administration abusing its power. But later in the year, she forcefully rejected a Trump administration proposal for a compact with colleges and universities that floated tying research funding to ideological alignment.

At the time, Dr. Paxson said she was worried that the compact “would restrict academic freedom and undermine the autonomy” of Brown.

(Hours before Dr. Paxson’s announcement on Monday, the administration effectively abandoned talk of a compact and encouraged universities to detail on their websites how they are responding to a litany of complaints about higher education.)

Brown’s year of turbulence turned to tragedy in December, after a former Brown student opened fire on campus, killing two and injuring nine others. As Dr. Paxson tried to lead the university through the aftermath, her leadership came under scrutiny, especially over the school’s approach to securing its campus in Providence, R.I., where visitors have long had easy access.

Brian T. Moynihan, the Bank of America chief executive who is the university’s chancellor, said Dr. Paxson had led Brown through its challenges with a “balance of commitment to academic excellence, operational excellence and a collaborative philosophy.”

Mr. Moynihan signaled that the cycle of strategic planning had played a role in the timing of Dr. Paxson’s exit. He added that there would be a national search for the next president.