He was the fifth CEO of the NCAA; he was named as the incoming president on April 27, 2010, and assumed his duties on November 1, 2010, and remained in office until March 1, 2023.

Emmert was previously the 30th president of the University of Washington, his alma mater, taking office in June 2004, becoming the first alumnus in 48 years to lead UW.

The NCAA ruled that Montana State was guilty of a "lack of institutional control" in 1993, stemming from behavior that occurred before Emmert arrived at the university.

The ruling was reached at the time Emmert belonged to the university's senior management team, along with Jim Isch, a former NCAA official.

These issues, which included more than $100 million lost due to mismanagement and more than a hundred fire and safety code violations, did not come to light during Emmert's tenure.

The NCAA accepted LSU's finding and self-imposed minor penalties (loss of two football scholarships) and declined to put the school on probation.

During the case, an employee of the academic counseling center confirmed the women's claims under oath, including changed grades for football players.

The UW Seattle campus was expanded with the purchase of the Safeco tower and property in the University District, adding about 500,000 square feet (46,000 m2) of building space.

With Emmert as President, new facilities were created for the Foster School of Business, molecular engineering, bioengineering, and residential halls.

Emmert initiated an annual summit with the Native American tribal council leaders from throughout the State of Washington and the region to address educational and health concerns.

Emmert was amongst the first 20 to sign the American College & University Presidents' Climate Commitment and is an active member of its steering committee.

[8] During Emmert's tenure, UW received more than $1 billion in grant and contract research funding for the fiscal year that ended June 30, 2007.

In August 2007, Emmert announced that UW would open an office in Beijing to lay the groundwork for expanding the university's presence in China.

[9] Emmert made the announcement during a campus visit by Zhou Wenzhong, ambassador of the People's Republic of China to the United States.

Emmert emphasized efforts to improve UW's environmental sustainability efforts throughout his tenure, leading to the university being recognized nationally as one of the most Eco-friendly campuses In January 2007, the fundraising goal for Campaign UW: Creating Futures was increased to $2.5 billion after the campaign reached its initial $2 billion goal 17 months ahead of schedule.

[14] In 2009, a year in which he turned down a pay increase offered by the Regents, Emmert's base salary at the University of Washington was $620,000 per year, but his total compensation package, including deferred compensation, was $906,500 annually, which made him the second highest-earning public university president in the United States, behind Ohio State's Gordon Gee.

In January 2018, a misleading 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.

[16] Subsequent reporting in multiple outlets pointed out that the suggestion that Emmert had been "personally informed" was actually a misleading reference to widely publicized accounts coming from Michigan State during 2010.

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.

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.

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.

[23] Emmert, however, was criticized over the Penn State case after internal emails surfaced revealing NCAA officials bluffed the university into accepting sanctions.

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.

[25] 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.

"[27] On May 5, 2016, a Pennsylvania judge, Gary Glazer, barred Penn State from receiving insurance coverage to pay settlements to Sandusky's accusers.

[28] 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."

"[29] 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.

While well-intended, the hashtag was quickly used by the public to air grievances about NCAA actions and express general disapproval with Emmert's presidency.