Kelly told the newspaper that he is undergoing an eight-week treatment for the methicillin-resistant Staphylococcus aureus (MRSA) infection that includes intravenous antibiotics three times a day.
"It's a small setback, but you have to keep pushing on, keep fighting and just live every day because you never know what tomorrow holds," Kelly told WQAM radio Saturday. "You got to keep a positive spirit. Anytime that you're fighting something you have to keep pushing on and have good people around you, and I have."
After months of chemotherapy and radiation treatment for jaw cancer, Kelly's doctors said in August that the Hall of Fame quarterback was no longer experiencing pain in his jaw. Further biopsies in September found no evidence of cancer.
That pain has now returned, Kelly explained to the Herald.
"I was cleared in September of the cancer -- I have another MRI in two weeks," Kelly told the newspaper. "The toughest part for me was I was almost ready to take out my feeding tube, I was feeling good and they said they need to do some biopsies. Those 12 biopsies put me back so far."
Kelly underwent further surgery after the biopsies and remains on a feeding tube.
The former University of Miami star returned to his alma mater Saturday to serve as an honorary captain for the Hurricanes' game against North Carolina.