The defender is a free agent this summer but has decided to call time on his Glovers career after two years and look for a club closer to his hometown of Carlisle.
Manager Gary Johnson acknowledges Huntington's departure is a setback but has already lined up defensive reinforcements.
Johnson told the club's official website: "Naturally I'm disappointed that Paul has decided to move on but I did feel he would end up moving back up north. He has been away from home for a while now and his expected decision has given me the opportunity to look at other options.
"I am happy with those options and when everything has been agreed and at an appropriate time I will reveal the name of the new centre-half.
"I'd like to take the opportunity to thank Paul for his time at Yeovil and wish him all the best for the future at wherever he continues his career."