Levin, 65, has served the institution longer than any other president currently in the Ivy League. His legacy extends well beyond Yale, with several of his administrators going on to lead top universities such as Duke, MIT, Oxford and Cambridge.
Levin, who plans to take a sabbatical and write a book, also left a major impact on New Haven as Yale became a major retail landlord and began a home ownership program and a college scholarship program for local high school graduates.
Yale's endowment went from $3.2 billion when Levin was named president to $19.4 billion this year. Levin helped raise more than $7 billion during his tenure, Yale officials said.
"He transformed the university in so many ways," said Yale trustee Indra Nooyi, chief executive of PepsiCo. "I'd say that Rick Levin will go down in history as one of the greatest presidents that Yale ever had."
Levin is credited with leading the school's largest building and renovation program since the 1930s. Yale renovated all 12 of its residential colleges and has plans to build two more. About 70 percent of the space on campus has been partially or comprehensively renovated since 1993.
Under Levin, the university improved its historically difficult relationship with its unions by securing long-term contracts. A homebuyers program started in 1994 offered financial incentives to Yale employees to buy homes in the city, and more than 1,000 faculty and staff have participated, Yale officials said.
In 2008, Yale announced what it called the largest increase in financial aid spending in its history, reducing the average cost by more than half for families with financial need, university officials said.
Levin said Thursday that the initiative "made a huge difference in the kind of students we can attract, the very best and brightest from all segments of society and from all around the world."
Yale's percentage of international students went from 3 percent to 10 percent as it offered financial aid to foreign students as well. All students were offered opportunities to study or work abroad, Yale offered leadership education for international officials and emerging leaders and its professors worked with faculty in China and other countries.
A planned joint campus with the National University of Singapore will open next year, and Levin predicted it will become a model for higher education in Asia.
Levin said he is leaving Yale with no regrets.
"It's just been an amazing run," Levin said. "We've accomplished so much in strengthening Yale's programs and in building Yale's position as a global institution."
Last year, students filed a complaint with the U.S. Department of Education that Yale failed to properly respond to sexual harassment. Department officials raised concerns with how complaints were handled in the past but praised the steps the university has taken.
Levin noted the department found no violations and said it was an opportunity to make significant changes.
Yale Corp., the university's governing body, will conduct a search for Levin's replacement. The last Yale president to serve 20 years was Arthur Twining Hadley, who took office in 1899.
Levin, who was born and raised in San Francisco, met his wife, Jane Levin, at Yale.
"From the day Jane and I entered graduate school in 1970, Yale has been our life," he wrote in a message to the Yale community.
Levin was an economics professor when he was tapped to become president in 1993. His wife is a senior lecturer, and the couple live in New Haven, where they raised four children.
When Levin took over, Yale's Gothic buildings were deteriorating, a budget deficit divided the campus and urban blight and crime encroached.
Law professor and former law school dean Tony Kronman called it a time of anxiety at the university, where there was "a mood of malaise within the faculty, an uncertainty as to whether we would be able to maintain our position of pre-eminence." He said Levin quickly showed a steady hand and patience and persistence.
"The most remarkable thing to my mind," Kronman said, "is just his steadiness of purpose day in and day out, year after year."