Kelly was drafted in the 33rd round of the 2005 MLB June Amateur Draft out of Chandler –Gilbert Community College. His professional debut came with the Rookie Greeneville Astros where he went 4-0 in 20 games with a 3.66 ERA. After a good rookie season, Kelly was promoted to the single-A affiliate Lexington Legends where he spent the 2007 and 2008 seasons.
In his second year with the Legends, Kelly reduced his ERA to 3.41 with a 3-3 record and 4 saves. Almost doubling his work load as a reliever Kelly averaged 9.1 strikeouts per 9 IP ringing up 72 batters in 2008. He was promoted again in 2009 as he joined the Lancaster Jethawks, high-A affiliate of the Astros where he posted a 2-1 record in 21 games including three starts.
Kelly joined a new organization in the Chicago White Sox where he spent the season with the Kannapolis Intimidators in 2011. In 11 appearances Kelly compiled a 3.72 ERA, 22 strikeouts, and a 1-0 record. In his final year at Chandler-Gilbert Community College Kelly led the team with 54 IP and a 2.00 ERA in nine games. He struck out 49 batters while posting a 4-2 record for the Coyotes.