Thompson was left unprotected by the Washington Nationals, who acquired him from Florida for first baseman Nick Johnson in 2009. Thompson, who made 26 starts at Double-A Harrisburg last season, was a first-round pick by the Marlins in 2005.
The Pirates also signed infielder Garrett Atkins to a minor league contract and invited him to their major league spring training camp. Atkins played for the Rockies from 2003-09.
In a minor league trade, the Pirates acquired infielder-outfielder Corey Wimberley from Oakland for right-hander Ryan Kelly. Wimberley led the Pacific Coast League with 56 stolen bases while hitting .284 for Sacramento last season.