National Collegiate Athletic Association
On April 27, 2010, Emmert was named president of the National Collegiate Athletic Association, headquartered in Indianapolis. He assumed his duties on November 1, 2010, and remained president until his retirement in March 2023.
As NCAA president, Emmert created the position of chief medical officer (CMO) of the NCAA and the Sports Science Institute. Hainline has worked with member schools to establish new protocols and research efforts to improve student health and wellness. In 2014, the NCAA entered a partnership with the Department of Defense for the largest longitudinal study of concussion and head trauma in history, funded initially by a $15 million contribution from the NCAA and $15 million from the Department of Defense. Funding has now surpassed $64 million and reached 50,000 students making it by far the most important research on head trauma in the world. Emmert’s advocacy for the health and wellbeing of athletes has also led to extensive efforts regarding mental health and the reduction of sexual assault.
In 2014, the NCAA Division I member universities, with Emmert's support, voted to change the system used to set their rules and policies so as to include greater input from athletic directors, faculty members, and senior women's athletics, and student athletes themselves, in addition to the university and college presidents who are ultimately responsible for all policy and governance decisions. In 2012 the colleges and universities approved substantial changes to the compliance and oversight policies of the Association. Among other improvements, under Emmert's tenure, the Committee on Infractions, the body that determines penalties and sanctions for rules violations, was expanded to include former university presidents and legal scholars, among others, thereby improving the efficiency and effectiveness of their work.
In January 2018, a media story implied that Emmert had been personally informed in November 2010 – six months after he was hired as the NCAA's president – of 37 reports involving Michigan State University athletes sexually assaulting women. Throughout his tenure, Emmert has led multiple efforts within the NCAA to confront sexual violence within higher education.
On April 26, 2022, Emmert announced he would step down no later than June 2023. That December, Former Massachusetts governor Charlie Baker was announced as Emmert's successor effective March 1, 2023.
During Emmert's tenure, Pennsylvania State University was rocked by the Jerry Sandusky sex abuse scandal. Sandusky, a former assistant football coach at Penn State, was accused and later convicted of sexually abusing several children, including those he had taken to the Penn State athletic facilities. He was also accused of using his access to the Penn State football program as a way of luring victims. The University Board removed the President, Executive Vice President, Athletic Director, and head football coach because of their handling of the Sandusky matter. The media outcry over the scandal was enormous. In response to the uniqueness of the Penn State case and the nature of the allegations, the NCAA Executive Committee and Emmert agreed with the University that Penn State should be allowed to conduct its own inquiry into the scandal.
In July 2012, former FBI Director Louis Freeh reported to the Penn State board that many serious missteps within the university administration and football program had occurred. Based upon the Freeh report, as well as material made public through the criminal processes, the NCAA Executive Committee, a group of 20 university and college presidents and senior leaders, along with the Division I Board of Directors, also a group of university presidents, agreed to a series of sanctions. They empowered Emmert to enter into an agreement with the Penn State leadership to jointly accept a consent decree.
Ed Ray, Executive Committee chair at that time and Oregon State president, said that while there has been much speculation on whether the NCAA had the authority to impose any type of penalty related to Penn State, the Executive Committee concluded that the egregious behavior not only goes against the NCAA's rules and constitution, but also against its values.
While many in the media called for Penn State football to receive the so-called "death penalty", the Executive Committee and Emmert instead entered into the consent decree with Penn State leadership that included imposing a $60 million fine to be used to fund nonprofit organizations that combat child sexual abuse, a multi-year reduction in football scholarships, a multi-year postseason ban on football, a vacation of wins from the formal record book for the period during which Sandusky was believed to have been engaging in sexual abuse of children, and the imposition of an Athletic Integrity Agreement, which was monitored by former Senator George J. Mitchell. The Big Ten conference, which includes Penn State as a member, also imposed sanctions on the university as a result of the scandal. The outcome was highly controversial among those who sought harsher punishment and those who sought greater leniency. Supporters of greater leniency argued that the basis of the consent decree, the Freeh Report, was overreaching and not supported empirically. Freeh has vigorously defended the report and its conclusions. He is being sued for defamation by Graham Spanier, the former president of Penn State. Spanier, along with two other former Penn State executives, were found guilty of criminal charges. Critics accused Emmert and the NCAA Executive Committee of a "rush to judgment" that did not provide sufficient due process even though the university itself agreed to the settlement agreement.
Emmert, however, was criticized over the Penn State case after internal emails surfaced revealing NCAA officials bluffed the university into accepting sanctions.
Several legal actions have occurred since the Penn State scandal was uncovered, some involving Penn State, Emmert, and the NCAA and its members; others have been focused on the university itself as it made restitution with the victims of the scandal. A legal suit was brought against Penn State and the NCAA by Pennsylvania Senator Jake Corman regarding where the funds from the fine should be spent. The case was ultimately settled by an agreement that the funds could be spent on child sexual abuse prevention within the Commonwealth of Pennsylvania and that the wins that had been vacated from the record book be restored. Major news media outlets both praised and criticized Emmert and the NCAA. Many writers that called for aggressive sanctions against the university, including the so-called death penalty, were disappointed that the NCAA had reduced its sanctions, while other were critical of their "rush to judgment" and started asking whether the culture at the NCAA was broken under Emmert's leadership. His presidency has been called "feckless, arrogant, self-aggrandizing, inept" and operating under "tortured logic."
On May 5, 2016, a Pennsylvania judge, Gary Glazer, barred Penn State from receiving insurance coverage to pay settlements to Sandusky's accusers. The judge pointed to the university's "negligent employment, investigation, and retention of Sandusky", adding that, "When he abused children...he was still a PSU assistant coach and professor, and clothed in the glory associated with those titles, particularly in the eyes of impressionable children. By cloaking him with a title that enabled him to perpetrate his crimes, PSU must assume some responsibility for what he did both on and off campus." PSU at that point had paid out $93 million to more than 30 Sandusky accusers.
On October 27, 2016, Mike McQueary, the former assistant coach who reported to Joe Paterno that he had observed Sandusky sexually assaulting a child in the team's showers, was awarded $7.3 million by a Pennsylvania jury, to be paid by Penn State for defamation. Shortly thereafter on November 20, 2016, the judge in the case, Thomas Gavin, ruled in favor of McQueary's whistleblower claim and added another $5 million to the jury verdict. In a rebuke to PSU, Gavin wrote, "Only when the 'Sandusky Matter' became public was Mr. McQueary subjected to disparate treatment and adverse employment consequences." The university, he stated, had imposed "the equivalent of banishment" on McQueary, including "being told to clean out his office in the presence of Penn State personnel, an action that suggests he had done something wrong and was not to be trusted."
On June 2, 2017, in the remaining criminal cases all three of the university's administrators – Spanier, Schultz, and Curly – originally implicated by the Freeh Report and the grand jury were found guilty of child endangerment by the State of Pennsylvania and sentenced to jail time. The judge in the case, John Boccabella, when announcing the sentences said, "Why Mr. Sandusky was allowed to continue to go to the Penn State facilities is beyond me. All three ignored the opportunity to put an end to [Sandusky's] crimes when they had a chance to do so." Boccabella also criticized deceased head coach Joe Paterno, saying he "could have made that phone call without so much as getting his hands dirty. Why he didn't is beyond me."