For years the NCAA, the governing body of collegiate athletics, has been the sports version of the Internal Revenue Service, a bureaucratic entity that is feared and loathed, full of mystifying guidelines and compassionless actions.

Few entities in sports have consistently generated as much bemusement or scorn for their decisions, but NCAA president Mark Emmert wants to turn the opaque into the open in the Kremlin of college sports. The 59-year-old Emmert, who became president in 2010, is the genteel leader of the kinder, gentler, more empathetic NCAA.

He says things you wouldn’t expect to hear from the head of the NCAA. He believes the rulebook needs to be half as thick and packed with twice as much common sense. He thinks that ensuring institutional integrity and morality is more important than upholding a picayune rule that makes accepting a bagel with cream cheese an NCAA violation. (That is an actual NCAA rule, folks.) He is convinced that a school providing a college athlete with minor compensation beyond room, board, and books isn’t anathema. And he acknowledges that the current structure of college football might have to change to accommodate mega-conferences that have overrun the landscape like weeds.

Emmert, who was in Boston to address some member schools, stopped by the Globe offices Thursday and talked about many issues in college sports. The former University of Washington president and Louisiana State and University of Connecticut chancellor is both a sports fan — he reminisced about the first time he saw Ray Allen’s “elegant” jumper at UConn — and a fan of providing more transparency.

“If we don’t go out there and explain what we do and who we are, I’ll have people think I’m [NFL commissioner] Roger Goodell, instead of [former United Nations Secretary General] Kofi Annan,” said Emmert. “I’m the guy that gave the press conference, but it wasn’t me that punished Penn State. It was the 1,100 member schools . . . Unless we let somebody come in and see what our enforcement process looks like, they think it’s this black box with whips and chains or arbitrary and capricious.”

I thought it was all of the above; just kidding, Mr. Emmert.

Emmert said the NCAA is overhauling its infractions process; instead of just two categories of violations (secondary and major), there will now be four categories, and violations will be divided into ones where a school is deemed responsible and ones where specific persons are held accountable. Those changes will be voted on next month.

The NCAA is also rewriting its rulebook. It will be presented in January and likely voted on in April. Most college sports fans would prefer the rulebook be used as kindling at one of those famous Texas A&M bonfires. Emmert understands.

“We have a 450-page rulebook that is filled with things that are anachronisms, that are counterintuitive, that are unenforceable,” said Emmert. “They just don’t make sense in a 21st century context.

“We’ve got to get the rules to focus on the things that really matter, the things that are a real threat to integrity, the lying, cheating, stealing kind of issues. And not be worried about spread on bagels and the size of envelopes.

“By this time next year, I’d love to chat with you again about the new Division 1 rulebook, and it better be half as big and twice as focused.”

Hallelujah. Providing the NCAA with a logical, fair-minded rulebook would be an accomplishment worthy of Nobel Prize consideration.

We often hear about player’s coaches; well, Emmert seems to be a player’s president. While he is a staunch proponent of the NCAA’s mission and its commitment to amateurism, he knows that allowing a school to provide an athlete with money to buy a large pizza is not the end of Western civilization.

Emmert advocated for what he called a “miscellaneous expense allowance,” a term he said comes from academia. That means some of that $10.8 billion the NCAA and its member schools get for the bacchanalia of college basketball known as the NCAA men’s basketball tournament would be funneled back to those who make it such a lucrative event to cover things like clothing, travel to and from school, dates on weekends, etc.

The number floated was $3,500, the average cost, Emmert said, for the 340 Division 1 schools in the NCAA. It’s not the pay some of these athletes deserve, not when their unctuous coaches — guys like Kentucky men’s basketball coach John Calipari ($4 million per year) and Alabama football coach Nick Saban ($5 million-plus) — are raking it in, but it’s progress.

“This isn’t pay. It’s about making sure the kid has got his real costs covered,” said Emmert. “That’s been very controversial, not with these [big-time schools] up here, but with these [lower-revenue schools] down here saying, ‘We can’t afford that.’ If you’ve got a $3 million budget you can’t afford that.

“If we can’t solve those kind of problems and make sure we’re providing kids with all the right kind of support as legitimate students, not paying them, but providing them with everything they need in support, then I think we’ve got a big issue. We have to be able to solve that problem.”

Imagine that, an NCAA president advocating for the student-athletes’ needs instead of just the institutions’.

Emmert certainly is not afraid to think outside the box. He showed that with the NCAA’s unusually swift adjudication in the Penn State/Jerry Sandusky scandal.

The actions the NCAA took in the case prompted some discussion as to whether the NCAA would police probity on a permanent basis.

The good news for Boston University hockey fans is that Emmert showed zero inclination that the NCAA was ready to get involved in the BU case. He said Penn State’s circumstances were unique and required unique action.

Emmert isn’t just changing the NCAA’s rules. He’s trying to change the way the NCAA rules.