Phegley started his professional career in 2009 at Single–A with the Kannapolis hitting .224 with 9 home runs and 33 RBI in 52 games.

Then during an injury-plagued 2010 season, Phegley spent time at three different levels in the White Sox system, rookie league Bristol, High–A Winston-Salem and Double–A Birmingham.

[8][9] In November 2010 surgery he had his spleen removed, because doctors were of the view that the non-vital organ which is mainly a blood filter was where his platelets were being destroyed.

Phegley spent the entire 2012 season at Triple–A Charlotte where he hit .266 with six home runs and 48 RBI over 102 games.

[10] On July 5, 2013, Phegley was promoted to the major leagues for the first time after hitting .316 with 15 home runs, 18 doubles and 41 RBI with Charlotte.

He collected his first major league hit and RBI on a single off of Tampa Bay Rays pitcher Jeremy Hellickson that same day.

[8] On December 9, 2014, the White Sox traded Phegley, Marcus Semien, Chris Bassitt, and Rangel Ravelo to the Oakland Athletics in exchange for Jeff Samardzija and Michael Ynoa.