He played in Major League Baseball (MLB) for the Pittsburgh Pirates, Toronto Blue Jays, and Philadelphia Phillies.

[1] After his senior season, the Texas Rangers selected him in the 28th round of the 2003 draft, but he elected to attend college rather than turning pro at that time.

[8] Scouts regarded Lincoln as one of the best players eligible for the 2006 draft, and the Pittsburgh Pirates chose him with the fourth overall selection of the first round, with the intention of advancing him through their system quickly.

An oblique strain limited him to 24 innings in 2006, and then he had Tommy John surgery on his right arm in April 2007, which sidelined him for the entire year.

In 2009, he started 13 games for the Double-A Altoona Curve of the Eastern League with a 1–5 win–loss record and a 2.28 earned run average (ERA).

[13] Lincoln earned his first Major League victory on June 30, 2010 by pitching a shutout against the Chicago Cubs at Wrigley Field.

Pirates General Manager Neal Huntington cited a drop in Lincoln's velocity since he was promoted and that he had strayed from his mechanics.

The Pirates optioned Lincoln back to Indianapolis the next day, when they recalled Chris Leroux to add depth to the bullpen.

[17] Lincoln made his Blue Jay debut on August 1, 2012, against the Seattle Mariners and threw 1.1 innings without yielding a hit.