Webb, 36, was 198-73 with four division titles in nine seasons with the Warriors, guiding them to the Class 4A championship series in his first season, 2004. Before that, he spent five seasons as coach at Smithville, posting a 69-33 record.
His 2012 team finished 19-8, giving him a final 267-106 mark.
"It was a tough decision, I'm definitely going to miss baseball," Webb said Monday night. "This is a good opportunity."
Webb has been working as an assistant principal at Pontotoc Junior High. His new job will begin on July 1.
"Coaching and working as an administrator, it's been the best of both worlds," Webb said. "I work for a great school district."
A native of Mooreville, Webb played for Rex Berryman's Troopers and said he quickly caught the coaching bug.
"I always enjoyed sports, always enjoyed baseball, and knew that was something I wanted to do," said Webb, who played at ICC, graduated from Mississippi State and did his graduate work at Ole Miss.
"Coaching in Smithville, that was a great town with great people. Then to come here to Pontotoc, I have loved every minute of it. I've had a lot of great players and I have to give them all the thanks."
March to the finals
His first year with the Warriors in 2004 - the team's first season in Class 4A - was a career highlight, Webb said.
For one thing, the team returned to its traditional home field - "The Hollow" - after being away for five seasons while it was being rehabbed.
"It was definitely special. We brought the field back to the high school, had a great group of seniors and a 25-game winning streak that took us to the state championship. We won Game 1 against Brookhaven, then lost the next two. But it was a great ride."
After that season, Webb was named the Daily Journal's Baseball Coach of the Year.
Webb said his former assistants, Dustin Payne and Andy McGregor, will direct Pontotoc's summer baseball team.