The new deal is an extension of the club's original five-year £10million deal signed in 2004, when the sports retailer became the official retail partner at Goodison Park.
Under the terms of the new three-year partnership JJB will take over the day-to-day running of Everton's retail operation from June 1, 2006.
Chief executive Keith Wyness said: "Retail is an extremely tough area of our business and by moving off in this particular direction it will benefit both the club and the customer.
"The competition in the industry is becoming increasingly tough and following our continued dialogue with JJB, as our retail partner, it became clear that their experience in retail meant this was a fantastic opportunity for us both."
JJB Sports is 39 per cent-owned by founder and former chairman David Whelan and his family. Whelan, who is executive director at JJB Sports, is also chairman of Everton's Premier League rivals Wigan.
