In a letter to the university's students, faculty and staff, Emmert said he had "mixed emotions" about leaving the school after five years on the Seattle campus.
"I am proud of the work we have done together and absent this truly extraordinary opportunity would have been happy continuing as president for many years to come," Emmert said.
He said leading the NCAA "offers a chance to shape the educational and athletic experiences of over 400,000 young people and to work with more than 1,200 universities, colleges and conferences to make intercollegiate sports a competitive, healthy, integral part of the growth and maturation of student-athletes."
USA Today reported the field of candidates to succeed the late Myles Brand as NCAA president included U.S. Sen. Evan Bayh, D-Ind., West Point Superintendent Lt. Gen. Franklin "Buster" Hagenbeck and Ernst & Young executive Beth Brooke, a former basketball player for Purdue University.
Emmert's appointment must be approved by NCAA's 18-member Executive Committee, the newspaper said.
Brand died of pancreatic cancer in September.