The 6'5", 230 pound Herndon was originally drafted by the Kansas City Royals in the 38th round of the 2004 amateur draft out of Mosely High School in Panama City, but did not sign. The following year, the Minnesota Twins drafted him in the 23rd round out of Gulf Coast Community College, but he again opted against signing. He ultimately signed with the Anaheim Angels after being drafted in the fifth round of the 2006 amateur draft.

Herndon began his professional career in 2006, going 5-2 with a 2.21 ERA in 14 starts for the Orem Owlz. In 2007, he went 13-8 with a 4.02 ERA in 25 games (24 starts) for the Cedar Rapids Kernels. He went 3-7 with a 5.01 ERA in 43 games (12 starts) in 2008 for the Rancho Cucamonga Quakes, and in 2009 he went 5-6 with a 3.03 ERA in 50 relief appearances for the Arkansas Travelers.

Herndon was selected by the Phillies in the 2009 Rule 5 Draft.

After the 2010 spring training, Herndon was selected for the Phillies' Opening Day roster. On April 5, he made his major league debut against the Washington Nationals. Through his first four outings he had not given up a run, but on April 16, he allowed four runs in ¹⁄₃ inning against the Florida Marlins. On July 27, Herndon picked up his first major league win versus the Arizona Diamondbacks. He ultimately earned a 1-3 record with a 4.30 ERA in 47 games; since he remained on the club's roster for the entire season, he continued in the Phillies' organization thereafter per Rule 5 regulations.

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