In January 2009, Cigarroa was appointed chancellor of the University of Texas System. He is the first Hispanic to ever lead a major university system in the United States. Before this appointment he had been the first Hispanic president of the University of Texas Health Science Center at San Antonio.
On July 1, 2010, Cigarroa began serving an elected six-year term as an Alumni Fellow to the Yale Corporation, the governing body of Yale University.
In August 2011, Cigarroa presented to the University Board of Regents his Framework for Advancing Excellence designed to make the University of Texas System one of the top-ranked US educational systems of higher learning. The framework was unanimously approved by the Board of Regents and has since received national acclaim. In December 2011, Cigarroa was invited to the White House to share his program with US PresidentBarack Obama and US Secretary of EducationArne Duncan.
On February 10, 2014, Cigarroa announced his resignation from the UT System.[4] His office forwarded third party letters of recommendations to the president's office at UT Austin, but he was not involved in overturning decisions made by the admissions committee.[5] He played a leadership role in uncovering admission wrongdoings at UT Austin by commissioning the Kroll Report.[6] He currently works as Director of Transplantation Services at the University of Texas Health Science Center San Antonio.