The Associated Press first reported on the conversation between Kelly and Sessions, on Wednesday. It follows a wave of criticism of Sessions by President Trump on social media and marks one of Kelly's first actions in his new role.
Sessions was among Trump's earliest and most vocal supporters during his campaign for president, endorsing him publicly in February 2016, and was widely regarded as a close ally of the president's going into his role as attorney general.
The relationship between the two men has shown signs of deterioration since Sessions recused himself from the Department of Justice's ongoing Russia investigation, with Trump calling his attorney general “beleaguered” in a tweet sent on July 24.
The reassurance from Kelly points to a change in direction from the ambiguous rhetoric the president used as recently as last week, when he said "time will tell" whether he will keep Sessions as attorney general.
ABC News' John Santucci contributed to this report.