Lincoln was examined on Monday by Dr. James Andrews, who conducted the reconstructive surgery in Birmingham, Ala.
"We anticipate Brad will be back sometime during the 2008 season," general manager Dave Littlefield said.
Lincoln tried to pitch early in spring training and again last week, and the latter attempt convinced the team to send Lincoln to Dr. Andrews.
Lincoln continues a remarkable string of bad luck for pitchers the Pirates have selected in the first round of the baseball draft.
Six of the last seven pitchers the Pirates have drafted in the first round have needed major surgery: Lincoln, Bryan Bullington, John Van Benschoten, Sean Burnett, Bobby Bradley and Clint Johnston.
Only Burnett and Van Benschoten have pitched in the majors, and Van Benschoten did so for only six games in 2004. He has been sidelined for most of the time since.
Lincoln was 12-2 with a 1.69 ERA for Houston last season before the Pirates made him the No. 4 pick in the June draft, paying him an estimated $2.75 million signing bonus. He was 1-2 with a 6.75 ERA in four games at Class-A Hickory before a rib cage injury ended his first pro season.