Eppler was hired as a scout for the San Diego Padres in 2000. He spent five years scouting for the Padres and Colorado Rockies. After the 2004 season, he was hired to scout for the Yankees, working in the Tampa office run by Mark Newman and Damon Oppenheimer. When Yankees General Manager (GM) Brian Cashman was given the authority to restructure the Yankees' front office after the 2005 season, he created a pro scouting department and promoted Eppler to run it. He was promoted to Assistant General Manager during the 2011–12 offseason.
Eppler is well versed in the statistics of baseball, using them to sign Edwar Ramírez out of independent baseball. He is considered by many, including Cashman and Gene Michael to be a future GM.
- Kepner, Tyler (February 28, 2009). "Yanks’ Top Scout Has Eye for Talent and Ear for Nuance". The New York Times. Retrieved October 24, 2011.
- Kepner, Tyler (September 22, 2006). "BASEBALL; From Arizona, to Columbus, to the Bronx". The New York Times. Retrieved October 24, 2011.
- Neyer, Rob (July 17, 2007). "Yanks use stats to find a gem". ESPN. Retrieved October 24, 2011.
- "Billy Eppler: Baseball America Executive Database". Baseball America. Retrieved October 24, 2011.
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