Urton received his B.A. from the University of New Mexico in 1969, and his M.A. and Ph.D. degrees from the University of Illinois Urbana-Champaign in 1971 and 1979, respectively. He was a professor at Colgate University from 1978 to 2002. He is married to artist and anthropologist Julia Meyerson.
Urton is a specialist in Andean archaeology, particularly the quipu (khipu) numerical recording system used in the Inca empire in the 15th and 16th centuries. Along with anthropologist Sabine Hyland, he is one of the most prominent advocates of the theory that the quipus encode linguistic as well as numerical information. From 2001 to 2005 he was a MacArthur Fellow.
According to an investigation by The Harvard Crimson, Urton was the subject of a sexual harassment complaint from a former student in 2016. The student alleged that Urton "pressured her into 'unwelcome sex'" in exchange for a recommendation letter. Urton responded that the allegations were "either untrue, inaccurate, or misleading". More allegations emerged following the publication of the investigation. UC-San Diego professor Jade d'Alpoim Guedes alleged that Urton had inappropriately propositioned her for sex while she was a graduate student at Harvard. It was also alleged that Urton harassed students at his field school in San Jose de Moro, and the anthropology department received further complaints that were not made public. In response, Urton was removed from his position as director of undergraduate studies and placed on administrative leave pending an investigation.
The allegations against Urton surfaced amidst reports of a general culture of sexual harassment and gender discrimination at Harvard's anthropology department. In 2015, while Urton was the chair of the department, a Title IX gender discrimination lawsuit was brought against it by former professor Kimberly Theidon. The lawsuit primarily concerned multiple allegations of sexual harassment against Urton's colleague Theodore C. Bestor, but also included the accusation that Urton had protected Bestor and "intentionally sabotaged" Theidon's application for tenure because of her advocacy for students who experienced sexual harassment. The complaints were dismissed by a federal court in 2018, with Judge Leo T. Sorokin writing that Urton had responded promptly and satisfactorily. In June 2020, the anthropology department acknowledged these were "long-standing problems" and formed a committee to address them.