In the newly created role, he will oversee the expansion plans for the three-year-old agency, whose clients include UKTV, BT and Norwich Union.
Clark stepped down as chairman of CMW in October 2006, 12 years after it was founded and two years after its £5m sale to Media Square.
He will continue running his own start-up branding consultancy, Onion, alongside his responsibilites for Crayon.
Richard French, Crayon managing partner, said: "Having Jonathan on board will help Crayon develop our business and brand in a more purposeful way.
"We have spent a good deal of time looking at our positioning and introducing more advanced business metrics to make sure we're running the business as efficiently as possible."
In a separate move, one of Crayon's founding directors has left the company to set up his own planning consultancy.
Omaid Hiwaizi, a former art editor for i-D magazine, started out as creative director for the agency before moving to the role of planning director.