Shortly after taking office, university president Joel Seligman commenced the private phase of the Meliora Challenge, a $1.2 billion capital campaign, in 2005. The campaign reached its goal in 2015, a year before the campaign was slated to conclude. In 2016, the university announced the Meliora Challenge had exceeded its goal and surpassed $1.36 billion. These funds were allocated to support over 100 new endowed faculty positions and nearly 400 new scholarships.

On September 1, 2017, a complaint was filed by eight current and former faculty members at the University of Rochester with the United States Equal Employment Opportunity Commission (EEOC). The complaint includes allegations of sexual misconduct/harassment perpetrated by Florian Jaeger, a tenure track faculty member, and condemnation of the response of University administration. The university’s initial public response to the complaint was a claim that the allegations were thoroughly investigated and could not be substantiated. Later, the university’s board of trustees announced a new, independent investigation into the allegations. The Board retained Mary Jo White, Senior Chair of Debevoise & Plimpton LLP and past United States Attorney for the Southern District of New York and Chair of the Securities and Exchange Commission, to lead the investigation. On January 11, 2018, the Debevoise & Plimpton released the report and held a press conference about the findings of the independent investigation. The team found the individuals covered in the report had not violated policy; however, significant recommendations were made to push the university towards leadership in policy regarding relationships between faculty, staff, employees, and students.

On the same day as the release of the report, university president Joel Seligman publicly announced his previously tendered resignation. Board chair Danny Wegman accepted the resignation and tapped Richard Feldman, Professor of Philosophy and previous Dean of the College, to serve as interim president.

On December 8, 2017 nine plaintiffs in the 2017 EEOC complaint filed a lawsuit with attorney Ann Olivarius against the university and two university employees in the U.S. District Court for the Western District of New York (Case No: 6:17-cv-06847, Aslin et al. v. University of Rochester et al.). Allegations in the lawsuit include a number of the matters raised by plaintiffs in the EEOC complaint. The plaintiffs seek “damages in an amount not yet quantified but to be proven at trial, for costs and attorneys’ fees, and for any other and further relief which is just and proper.” After Lawrence Vilardo, the federal judge hearing the case, upheld the legal validity, in whole or in part, of 16 of the 17 claims in the lawsuit, the parties in March 2020 agreed to a settlement in which the University of Rochester paid $9.4 million to the plaintiffs, with the plaintiff Jessica Cantlon (now of Carnegie Mellon University) writing, “We consider it a major victory for all of the faculty and students who were harassed,” and “[the settlement is] going to have a really powerful impact on how seriously universities take women who come forward with complaints of sexual harassment. This is something that universities will notice.”