The letter does not detail specific infractions or penalties.
The investigation into the football program began in June 2010 after more than a dozen players were accused of accepting gifts from or having inappropriate contact with possible NFL agents. Those accusations resulted in the resignation of associate coach John Blake, who had ties to NFL agent Gary Wichard.
The NCAA ruled several players ineligible to play while others were cleared of wrongdoing.
Director of Athletics Dick Baddour says the university is cooperating with the NCAA.
"The notice of inquiry is a formal notification from the NCAA that they have been reviewing our football program," Baddour said. "We have been working with the NCAA and cooperating with them on this investigation. We are committed to the process and will continue to cooperate."
UNC says if it receives a notice of allegations, it will make the notice available on TarHeelBlue.com.