Drafted by the Baltimore Orioles in the 15th round of the 2011 MLB Draft from Central Arizona College (Coolidge, AZ). Spent 2011 in the Florida Gulf Coast League with the Orioles, throwing in four games and holding a 3.52 ERA. Pitched 7.2 innings and struck out six.
In 2012, started with the Florida Gulf Coast League Orioles, before getting called up to the single-A Delmarva Shorebirds of the South Atlantic League. After posting a 2-0 record and 0.00 ERA in three games with the GCL Orioles, Wooten put up a 2-3 record with a 3.46 ERA in Delmarva. Started in two of his 11 appearances and threw 39 innings while striking out 30 and walking just six.