Barchi's appointment comes as the much-disputed merger of Rutgers-Camden and Rowan University remains on the table - a project pushed by Gov. Christie.
Barchi, a nueroscientist, has spent his career in Philadelphia, previously serving as a faculty member and then provost of the University of Pennsylvania.
Officials praised Barchi's background.
"Robert Barchi combines the key qualifications that are necessary to serve as the next president of Rutgers," said Ralph Izzo, chair of the Board of Governors, in a prepared statement. He cited Barchi's "successful tenure leading a highly regarded health sciences university; years of experience as the chief academic administrator of a world-class comprehensive research university; and a stellar reputation as a scientific researcher and an award-winning educator."
More than 250 people were nominated for the job, about 70 of them considered.
Barchi received his bachelor's and master's degrees from Georgetown University and his doctorate and medical degrees from Penn. He began his career as a faculty member at Penn in 1972 and was named provost in 1999.
During his time at Jefferson, the university expanded from three to six schools, increased enrollment by 51 percent and doubled fundraising, according to a press release from Rutgers.
He is married to Francis Harper Barchi, a senior fellow in the Center for Bioethics at Penn.
Contact Susan Snyder at 215-854-4693 or ssnyder@phillynews.com, or follow on Twitter @ssnyderinq