He debuted professionally a year later with the GCL Twins, reaching base safely in 19 straight games at one point.

After two seasons with the New Britain Rock Cats and appearances for the 2007 and 2008 Eastern League All-Star team, he was promoted to AAA with the Rochester Red Wings.

In his first Major League at bat he hit a home run against Detroit Tigers pitcher Max Scherzer.

Six other Twins have homered in their first at-bat: Rick Renick (1968), Dave McKay (1975), Gary Gaetti (1981), Andre David (1984), and Eddie Rosario (2015).

On April 22, 2012, he was claimed off of waivers by the Oakland Athletics to make room on the Twins roster for RHP Jason Marquis.

On June 8, 2015, Hughes signed with the Lancaster Barnstormers of the Atlantic League of Professional Baseball and finished out the season with the club, hitting .240/.308/.422 in 78 games with 12 homeruns.

After debuting for the Western Heelers in the 2002 International Baseball League of Australia season being named in the post-season All-Star team at second base as a 17-year-old.

In 2010, the Australian Baseball League was formed and Hughes fresh off his MLB debut was the biggest name on the Heat roster.

For the 2018–19 Australian Baseball League season, Hughes along with Heat teammate Allan de San Miguel moved to the Melbourne Aces.