Thornton will take over as permanent head coach of the Bobcats on Jan. 15, pending the approval of the school’s board of trustees.
Thornton has served as offensive coordinator, quarterbacks coach and recruiting coordinator for the past two years at JCJC.
Thornton succeeds Ray Perkins, who resigned in December after two years as head coach of the Bobcats. Perkins guided the Bobcats to a 15-5 record, including the MACJC South Division title in 2013.
Thornton came to JCJC after serving as offensive coordinator at Southwest Mississippi JC from 2008-11.
He served as offensive coordinator at Middle Georgia Junior College from 1998-2000. The Warriors were 27-8 and won two NJCAA bowl games.