Yeshiva University said on Thursday that it would recognize an L.G.B.T.Q. student club on campus, bringing to an end a bitter yearslong legal battle over whether the school could deny the group official recognition on religious grounds.

Yeshiva, a Modern Orthodox Jewish institution with campuses in Manhattan and the Bronx, had refused for years to recognize the club, which had been known as the Yeshiva University Pride Alliance. The case made its way through state and federal courts, even reaching the U.S. Supreme Court, and was closely watched by religious organizations and religious freedom groups.

But on Thursday, its administration said in a statement that it and the students had “reached an agreement, and the litigation is ending.” As part of the settlement, the students said the Pride Alliance would be renamed Hareni, a religious term they had suggested.

In a statement, the school said the club “will seek to support L.G.B.T.Q. students and their allies and will operate in accordance with the approved guidelines of Yeshiva University’s senior rabbis.”

It added: “The club will be run like other clubs on campus, all in the spirit of a collaborative and mutually supportive campus culture.”

The battle at Yeshiva University had brought one of the country’s most liberal cities to the front line of a nationwide debate over religious freedom and civil rights and whether houses of worship, religiously affiliated organizations or even pious individuals could be compelled to provide public accommodations to people with differing views.