In July 1986, Wefald began his service as president of Kansas State University. Wefald held the second-longest term of any Kansas State President, trailing only the 25-year tenure of James McCain. During his tenure at K-State, over of new buildings were built, private giving increased from $6 million a year to nearly $100 million a year, research funding increased from $18 million to $110 million a year, enrollment increased from 17,000 to 23,000, and, finally, K-State students won 125 Rhodes, Marshall, Truman, Goldwater, and Udall Scholarships from 1986 to 2008—more than any public university in America.
Post-retirement
Wefald announced on May 12, 2008 that he would retire at the end of the 2008-2009 academic year. Subsequently, a routine audit performed by the Kansas Board of Regents determined that during Wefald's tenure a total of 13 undocumented payments had been made to former head football CoachBill Snyder, former athletic director Tim Weiser and Bob Krause, a former vice president and athletic director at the university. Combined, these payments amounted to $845,000. Additionally, a plan was uncovered during the audit to "funnel more than $3 million in deferred compensation to former football coachRon Prince." On May 20, 2009, Kansas State University and its athletic corporation filed suit to have a secret agreement between Prince and Krause declared invalid. Prince filed a lawsuit against the university which included the claim that Wefald and other high-ranking university officials had "actual or constructive knowledge" of the transaction. In May 2011, the lawsuit was settled and Prince received $1.65 million. Wefald denied any knowledge of this secret transaction, attributed the discrepancies to Krause, and immediately called for Krause to resign as director of economic development for the K-State Olathe Innovation Campus, which he did effective on May 20, 2009. In June 2014, the Kansas Board of Regents approved Kansas State University's request to name its new residence hall in Wefald's honor. Construction of Wefald Hall started in fall of 2014 and was completed in fall of 2016. In approving the university's request, Regents Chair Fred Logan said, "I think if you look at higher education Kansas, he was, it's fair to say, a historic figure. He was a historic president."