NCAA President Mark Emmert said, ‘These changes will help all our schools better support the young people who come to college to play sports while earning a degree.’ (David J. Phillip/ASSOCIATED PRESS)

The NCAA’s Division I Board of Directors voted through a new — and potentially groundbreaking — measure Thursday when it approved the “Big Five” athletic conferences’ ability to govern themselves and push through rules changes as they see fit.

After the board’s 16-2 vote in Indianapolis, five conferences: the Southeastern Conference, ACC, Big 12, Big Ten and Pacific-12 — will have autonomy to vote on prospective changes that could change the face of college sports.

One of the first topics expected to be addressed in the coming months is whether amateur athletes in the NCAA’s highest-revenue sports, namely football and men’s basketball, are entitled to additional benefits, including a stipend.

The vote centered on a model distributed recently to NCAA member schools that outlined new voting procedures and how proposed amendments can pass.

“The new governance model represents a compromise on all sides that will better serve our members and, most importantly, our student-athletes,” NCAA President Mark Emmert said in a statement. “These changes will help all our schools better support the young people who come to college to play sports while earning a degree.”

Thursday’s vote puts an effective end to the suggestion that all 351 Division I programs operate on a level playing field. Although administrators at some small schools were leery about what the new landscape means, many correctly predicted the vote would carry.

“Their business plan is in no way, shape or form like mine,” Mercer Athletic Director Jim Cole said this week. “I’m giving that. I want them to have some things to help them govern themselves better and run their businesses better. On the other side, I’m a little fearful of exactly what gets put in that autonomy. That right now is kind of the unknown.”

The NCAA’s authority has come under criticism recently, leading to several lawsuits, the most high profile of which was filed by former UCLA basketball player Ed O’Bannon. On behalf of all NCAA football and basketball players, O’Bannon’s suit challenged the organization’s use of players’ images for commercial purposes and argued the NCAA has violated antitrust law.

In late March, Northwestern football players were allowed to unionize, and recent talk about larger athletic departments requesting that Congress grant an antitrust exemption has raised questions about the future of amateur athletics and the NCAA as it has existed for decades.

Throughout the past months, the five power conferences spearheaded several proposals that led to Thursday’s vote. Some past proposals included a possibility that a simple majority was necessary to enact changes — a suggestion that made some administrators, particularly those at Football Championship Subdivision schools, uncomfortable. But as discussions intensified, the power conferences agreed to a fairer, if more complicated, voting process that makes significant change tougher to pull off.

If a rule is proposed, it can be passed in one of two ways: 60 percent of 80 eligible voters — including three student-athlete representatives from each conference — and a simple majority from three of the five conferences can pass it or a majority of all voters and a simple majority from four of the five conferences.

Any school can follow any new rule the Big Five passes, though smaller programs will often be at the mercy of their own budgetary restrictions.

“I’ll have to make a decision along with my conference, the Southern Conference: What can we afford to do?” Cole said. “Some of those big schools have 30, 40 academic advisers. I’ve got two. We have these 10 things we’re allowed to do now; we’ll do one and two.”

Division I schools can vote against the new model over the next two months, though it would take at least 75 schools to lead to a reconsideration and 125 schools to suspend the change. Some administrators disagree with the new measure; they assume it will lead to an even wider gulf between haves and have-nots and could bring on wholesale changes to amateur sports. Yet even critics have accepted autonomy is part of college athletics’ future.

Big Ten Commissioner Jim Delany said approval would give freedom to all schools to customize their athletic departments to their own needs and restrictions. If one program believes in one rule change or benefit more than another, for instance, it can adopt it as its needs dictate.

“Mostly in the student-athlete welfare category, where high-profile universities want to do more and can do more, there may be differences,” Delany said. “But even in that respect, [smaller schools are] not precluded from doing those things. You can just resource up. They can fundraise. They can do more at the gate. They can do more institutional support, if they want to do it.”

He said initial discussions about athlete benefits might not take place for months; he estimated that “substantial changes in the student-athlete experience” could be brought to vote in the next 18 months and could go into effect by the beginning of 2016.

“We’ve got a pretty aggressive set of challenges, I think, over the next year or so,” he said. “And it’s sort of like the dog catching the car. Now we’ve got to do something, you know?”