Skinner was appointed in 2021 and led the club to their first major trophy in women's football with an FA Cup triumph in 2024.
"Marc Skinner has departed his role as head coach of Manchester United Women by mutual agreement," the club said in a statement on Monday.
"Marc leaves having made a significant contribution to the continued progress of Manchester United Women."
United, who finished fourth, 15 points behind champions Manchester City in the WSL last season, launch their season at London City Lionesses on September 4th.