Clark, 41, graduated from Shannon in 1988 and played football at Mississippi State. He is currently an offensive coordinator at a high school in Tulsa, Okla.
Shannon athletics director Bill Rosenthal said the school received 25 applications and interviewed eight.
“It was a tough decision. We had really good applicants,” Rosenthal said. “He had more experience, is a little older and wanting to come back home and be part of the community.”
Clark, whose brother Dave is the third base coach for the Houston Astros, will arrive on April 27.
Shannon opens spring practice April 23 and will play a jamboree at Nettleton on May 11.
Cook was 48-16 in five seasons.