The First Baptist Church of Hamilton was founded in 1796; its leadership then founded the Baptist Education Society of the State of New York in 1817. From 1819-1846, the Hamilton Literary and Theological Institution existed as a proto-college to both Madison, renamed Colgate, University and the University of Rochester. This institution existed to train clergy in the Baptist tradition, but the academic leadership aspired to grant higher degrees and created a collegiate division separate from the theological division.
In 1846, the State of New York granted a charter to the collegiate division of The Hamilton Literary and Theologic Institution, which then sought help from the Columbian College in the District of Columbia, a fellow Baptist institution in the young nation's Capital. From 1846-1850, degrees issued by Madison University were awarded by Columbian College, which would become the George Washington University. At the urging of John Wilder and the Baptist Education Society, the university was to be moved to Rochester, New York. However, legal action prevented Madison from moving to Rochester.
In response, dissenting faculty, students, and trustees defected and departed for Rochester, where they sought a new charter for a new university.
Individuals important to the academic and financial health of the institution departed Madison for Rochester, including Asahel Kendrick. Kendrick, professor of Greek, served as acting president while the national search was conducted. He reprised this role until 1853, when Martin Brewer Anderson of the Newton Theological Seminary in Massachusetts was selected to fill the inaugural posting.
The University of Rochester's new charter was awarded by the Regents of the State of New York on January 31, 1850. The charter stipulated that the university have $100,000 in endowment within five years, upon which the charter would be reaffirmed. An initial gift of $10,000 was pledged by John Wilder, which helped catalyze significant gifts from individuals and institutions.
Classes began that November, with approximately 60 students enrolled, including 28 transfers from Madison. From 1850-1862, the university was housed in the old United States Hotel in downtown Rochester located on Buffalo Street near Elizabeth Street, today, West Main Street near the I-490 overpass. On a February 1851 visit, Ralph Waldo Emerson said of the university:
'They had bought a hotel, once a railroad terminus depot, for $8,500, turned the dining room into a chapel by putting up a pulpit on one side, made the barroom into a Pythologian Society's Hall, & the chambers into Recitation rooms, Libraries, & professors' apartments, all for $700 a year. They had brought an omnibus load of professors down from Madison bag and baggage... called in a painter and sent him up the ladder to paint the title "University of Rochester" on the wall, and they had runners on the road to catch students. And they are confident of graduating a class of ten by the time green peas are ripe.''
For the next 10 years, the college expanded its scope and secured its future through an expanding endowment, student body, and faculty. In parallel, a gift of 8 acres of farmland from local businessman and Congressman Azariah Boody secured the first campus of the university, upon which Anderson Hall was constructed and dedicated in 1862. Over the next sixty years, this Prince Street Campus grew by a further 17 acres and was developed to include fraternities houses, dormitories, and academic buildings including Anderson Hall, Sibley Library, Eastman and Carnegie Laboratories, the Memorial Art Gallery, and Cutler Union. 
The first female students were admitted in 1900, the result of an effort led by Susan B. Anthony and Helen Barrett Montgomery. During the 1890s, a number of women took classes and labs at the university as "visitors" but were not officially enrolled nor were their records included in the college register. President David Jayne Hill allowed the first woman, Helen E. Wilkinson, to enroll as a normal student, although she was not allowed to matriculate or to pursue a degree. Thirty-three women enrolled among the first class in 1900, and Ella S. Wilcoxen was the first to receive a degree, in 1901. Male students moved to River Campus upon its completion in 1930 while the female students remained on the Prince Street campus until 1955.
Major growth occurred under the leadership of Benjamin Rush Rhees over his 1900-1935 tenure. During this time, George Eastman became a major donor, giving more than $50 million to the university during his life. Under the patronage of Eastman, the Eastman School of Music was created in 1921. In 1925, at the behest of the General Education Board and with significant support for John D. Rockefeller, George Eastman, and Henry A. Strong's family, medical and dental schools were created. In that same year, the university award its first Ph.D.
During World War II, Rochester was one of 131 colleges and universities nationally that took part in the V-12 Navy College Training Program which offered students a path to a Navy commission.
In 1942, the university was invited to join the American Association of Universities as an affiliate member and it was made a full member by 1944. Between 1946 and 1947, in infamous uranium experiments researchers at the university injected uranium-234 and uranium-235 into six people to study how much uranium their kidneys could tolerate before becoming damaged.
In 1955, the separate colleges for men and women were merged into The College and located on the River Campus. In 1958, three new schools were created in engineering, business administration, and education. The Graduate School of Management was named after William E. Simon, former Secretary of the Treasury in 1986. He committed significant funds to the school because of his belief in the school's free market philosophy and grounding in economic analysis.
Financial decline and name change controversy
Following the princely gifts given throughout his life, George Eastman left the entirety of his estate to the university after his death by suicide. The total of these gifts surpassed $100 million, before inflation, and, as such, Rochester enjoyed a privileged position amongst the most well endowed universities. During the expansion years between 1936 and 1976, the University of Rochester's financial position ranked third, near Harvard University's endowment and the University of Texas System's Permanent University Fund. Due to a decline in the value of large investments and a lack of portfolio diversity, the university's place dropped to the top 25 by the end of the 1980s. At the same time, the preeminence of the city of Rochester's major employers began to decline.
In response, the University commissioned a study to determine if the name of the institution should be changed to "Eastman University" or "Eastman Rochester University". The study concluded that a name change could be beneficial because the use of a place name in the title led respondents to incorrectly believe that it was a public university, and because the name "Rochester" connoted a "cold and distant outpost." Reports of the latter conclusion led to controversy and criticism in the Rochester community. Ultimately, the name "University of Rochester" was retained.
In 1995, university president Thomas H. Jackson announced the launch of a "Renaissance Plan" for The College that reduced enrollment from 4,500 to 3,600, creating a more selective admissions process. The plan also revised the undergraduate curriculum significantly, creating the current system with only one required course and only a few distribution requirements, known as clusters. Part of this plan called for the end of graduate doctoral studies in chemical engineering, comparative literature, linguistics, and mathematics, the last of which was met by national outcry. The plan was largely scrapped and mathematics exists as a graduate course of study to this day.
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 that 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.
2017 US Equal Employment Opportunity Commission complaint
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 a tenure track faculty member and condemnation of the response of University administration. The university responded publicly that the allegations were thoroughly investigated and could not be substantiated. The public disclosure of the EEOC filing dominated the discussion at a regularly scheduled Presidential Town Hall Meeting and subsequent student protests included a campus rally and hunger strike. In November 2017, hundreds of academics in the brain and cognitive science, neuroscience, and psychology fields at other colleges and universities signed an open letter discouraging their students from seeking admission or employment at the university.
In response, the university's board of trustees announced an independent investigation into the allegations on September 19 and clarified the scope of the investigation and the composition of the committee on September 28, 2017. 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 slated to return their findings by the end of 2017. On January 11, 2018, the Debevoise & Plimpton released the report and held a press conference regarding the findings of the independent investigation. The team found that policy was not violated by the individuals covered in the scope of the report; 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. This action was accepted by board chair Danny Wegman, who then tapped Richard Feldman, professor of philosophy, to serve as interim president.