He then became the defensive coordinator at Henderson State in 1999. Kelly was the defensive coordinator and linebackers coach at Eufaula (AL) High School from 2000 to 2001. He was the defensive backs coach at Nicholls State from 2002 to 2003 and defensive coordinator there from 2004 to 2005. Charles then moved to Georgia Tech, where he was special teams coach from 2006 to 2007, cornerbacks coach from 2008 to 2009, and defensive backs coach from 2010 to 2012, as well as interim defensive coordinator in 2012. Kelly was the special teams and linebackers coach at Florida State in 2013 and defensive coordinator at FSU from 2014 to 2017. He was the special teams and safeties coach at Tennessee in 2018 before becoming assistant defensive coordinator and safeties coach at Alabama in 2019.