The deal, which is reportedly worth between £6m and £10m, will change the tournament's official title to the Carnegie Challenge Cup, after the university's Carnegie Faculty of Sport and Education.
The RFL claims the partnership is the first of its kind in England between a university and a national sports governing body.
Carnegie said its sponsorship of the Challenge Cup was part of its plans to become one of the UK's best-known university brands over the next six years, and hoped that the sponsorship would translate to opening athlete training facilities, branded courses and research centres.
Paul Kimberley, commercial director at RFL, said: "In 2004 we undertook an intensive market research-based review as the basis for a new marketing strategy to communicate the strength of Rugby League to key opinion formers and above all, to our loyal and potential new fans."
Leeds Carnegie's sponsorship of the RFL means it will join Engage and Gillette as Challenge Cup sponsors.
Richard Lewis, executive chairman of the RFL, added: "The RFL also believes elements of the partnership involving sports performance and academic study are tremendously significant and show the progressive nature of the sport and the university."
The tournament's final, which is held over the August bank holiday weekend, will be returning to Wembley this year.
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