Scorsese's new project marks his fourth production for the cable network.
Entertainment Weekly reports that the Clinton documentary will spotlight the former US president's time in the White House.
Speaking out about taking on the HBO project, Scorsese referred to Clinton as both an active and valid figure in the world of politics.
"A towering figure who remains a major voice in world issues, President Clinton continues to shape the political dialogue both here and around the world," Scorsese said of the new film.
"Through intimate conversations, I hope to provide greater insight into this transcendent figure."
[Former US president Bill Clinton on the campaign trail with President Obama]
Clinton seemed equally happy about working with the award-winning director on the documentary.
"I am pleased that legendary director Martin Scorsese and HBO have agreed to do this film," he said.
"I look forward to sharing my perspective on my years as president, and my work in the years since, with HBO's audience."