Ryan Richter, the head coach of the club's developmental team, Philadelphia Union II, was named Carnell's replacement on an interim basis.
The move came less than a year after Carnell led the Union to the best record in the MLS in his first season as head coach. Philadelphia was the top seed in the playoffs before being eliminated in the quarterfinals.
Carnell didn't make it halfway through his second year, as the team opted to make a move with the Union at 1-10-4, the worst mark in the 30-team league.
Union principal owner Jay Sugarman praised Carnell's professionalism and expressed confidence in Richter during the search for Carnell's permanent replacement.
Richter served as the first team's assistant head coach from 2022-24, before being appointed to serve as Union II's head coach in January 2025.
Scheer has been involved with the Union since 2018 and worked in various roles, including director of academy and professional development and most recently as interim sporting director.
The Associated Press contributed to this report.