Originally signed by the Philadelphia Phillies in 2003, he started his professional career off in 2004, where - with the GCL Phillies - he pitched in 12 games, starting 11 of them. He posted a 5-5 record with 62 strikeouts in 58 innings and a 2.79 ERA.
In 2005, Pichardo didn't fare as well as he had in 2004. He pitched in 10 games for the GCL Phillies, starting nine of them. He went 2-3 with 37 strikeouts in 54 innings and a 4.17 ERA.
On August 28, 2005, he was traded to the Giants for Michael Tucker.
He split time with the San Jose Giants and Connecticut Defenders in 2007. Used entirely as a reliever, he went a combined 4-5 with 87 strikeouts in 67 2/3 innings of work. In 46 games, he posted a 3.33 ERA with five saves.Overall, he has gone 16-16 with a 3.45 ERA in 86 minor league games (25 starts). He has struck out 245 batters in 232 innings, saving six games.