In February 2024, Eppler was placed on MLB's ineligible list for the 2024 season due to fabrication of player injuries in violation of league rules during his tenure with the Mets.

[5] After the 2004 season, he was hired to scout for the New York Yankees, working in the Tampa office run by Mark Newman and Damon Oppenheimer.

[5][7] In that role, Eppler and his staff were responsible for scouting acquisitions, which led to the signings of Bartolo Colón, Eric Chavez, Cory Wade, Freddy García, Russell Martin, Andruw Jones, and Luis Ayala.

[12] When the Arizona Diamondbacks fired Kevin Towers as their general manager in September 2014, Eppler was one of the five candidates they identified as a potential replacement.

[18] Later in October, the Angels lost front office executives Matt Klentak, Tim Bogar, and Scott Servais, who were hired by other organizations.

[19] Eppler developed his own analytics department, and brought some executives, including special assistant Eric Chavez, to the Angels from New York.

[18] Over the next few seasons, Eppler built around Mike Trout with acquisitions of Shohei Ohtani, Justin Upton, Anthony Rendon, and Andrelton Simmons.