Huppert reached the major leagues as a catcher with the Orioles in 1983 and again with the Milwaukee Brewers in 1985.

Huppert began his managerial career with the Helena Gold Sox in 1986 at the age of 29.

He went on to work in the farm systems of the Milwaukee Brewers (1986–91), Chicago White Sox (1993–98), Florida Marlins (1999–2001), Montreal Expos (2002–04), Philadelphia Phillies (2006–10) and Detroit Tigers (since 2011).

He worked alongside the legendary Frank Robinson as third base coach for the Washington Nationals during that team's inaugural season in 2005, after its transfer from Montreal.

Huppert was named Manager of the Year in 1988 with the Stockton Ports in the California League and in 2001 with Brevard County.