For the 2025 re-release of Backyard Baseball 2001 (a.k.a. Backyard Baseball '01), the professional MLB players Barry Bonds, Ken Griffey Jr., and Frank Thomas were replaced with the new characters Hugo Hernandez, Luke Lopez, and Chase Wilton respectively. This is due to the real-life players not granting permission to use their likenesses in the re-release; all three new characters were made using pre-existing characters from the custom character creator and share the same stats as the pros they replaced. As a result, the Chicago White Socks and San Fransisco Giants lack an official MLB player from their respective teams, though the Cincinnati Reds are still represented with the inclusion of Barry Larkin.

The 2025 re-release of Backyard Baseball 2001 (a.k.a. Backyard Baseball '01) changes the names of the Cleveland Indians and the Oakland Athletics to the Cleveland Guardians and Athletics respectively, and replaces their respective logos with new ones, reflecting changes made by the real-life baseball teams in the 2020's. The former reflects the 2021 rebranding of Cleveland's team after controversy surrounding its original name and former mascot Chief Wahoo, while the latter reflects the Athletics moving out of Oakland in 2025 and depreciating their association with any city until they completed their permanent move to a new ballpark in Las Vegas, Nevada. New voice lines were also recorded replacing all mentions of the Cleveland Indians and Oakland Athletics with the new team names. For unknown reasons, no other team names or logos were adjusted; the Montreal Expos are notably still present in the game, despite having moved to Washington, D.C. and renaming themselves as the Washington Nationals in 2005.