Seoul City Mayor Park Won-soon was found dead on Friday, South Korea’s Yonhap news agency reported, after his daughter reported him missing a day earlier.
The Seoul Metropolitan Police Agency found his body at Mt Bugak in northern Seoul, near where his phone signal was last detected during a late night search, Yonhap said.
No cause of death has yet been released.
It has emerged that a female employee had filed a sexual harassment claim against Mr Park in the hours before he went missing, but there has been no confirmation that this was a factor.
He did not show up for work on Thursday, cancelling a meeting with a presidential official at his Seoul City Hall office, Kim Ji-hyeong, an official from the Seoul Metropolitan Government, told the Associated Press.
Police officer Lee Byeong-seok told reporters that Park was seen by a security camera at 10:53 near the entrance to the wooded area where the phone signal was last detected.
About 600 police and fire officers using drones and dogs searched the area for hours on Thursday.
Crowds gathered outside the Seoul National University hospital late on Thursday amid unconfirmed reports that Mr Park had been found and taken there.