Werner was signed by the San Diego Padres as an undrafted free agent after the 2010 season.

In 2012, he pitched for the San Antonio Missions and the Tucson Padres before being called up to the majors for the first time on August 22, 2012.

[4] On November 16, 2012, Werner was traded to the Oakland Athletics with Andy Parrino for Tyson Ross and A.J.

[5] On December 4, 2013, Werner was designated for assignment by Oakland, to clear room on the 40-man roster for recently signed pitcher Scott Kazmir.

[7] Werner signed to play with the Ottawa Champions in the Canadian American Association of Professional Baseball in 2015.