Payne has presided at the Washington club since its inception in 1996 but has decided to part ways with some reports suggesting he could be on his way to Toronto FC.
"It goes without saying there will always be a part of me here at DC United," Payne said.
"My wife and I spent a lot of time talking about this, and I really think it's the right thing to do for me. And I do honestly believe it will be a good opportunity for DC United to maybe do things differently.
"The future of DC United will be in very good hands. I do think the new ownership (of Erick Thohir and Jason Levien, joining Will Chang) is stable, and they're ready to move things forward. Had it been in the recent past, I might not have felt comfortable moving."