Wilks was hired by the Chicago Bears on February 16, 2006. The Bears announced on December 30, 2008, that they had fired Wilks.
Wilks was not unemployed for long, however. He was hired as defensive backs coach of the San Diego Chargers in 2009 when former Bears defensive coordinator Ron Rivera moved to the same position in San Diego.
When Rivera became head coach of the Panthers, he hired Wilks as secondary coach on January 15, 2012. He was promoted to assistant head coach in 2015.