Stoltidis started out with Pontioi Kozanis FC in the fourth division before signing for Iraklis FC, where he spent eleven years. He made his Alpha Ethniki debut for the Thessaloniki-based club in December 1992 but did not become a regular until 1995–96. The following term he played UEFA Cup football for the first time. Stoltidis stood out in 2002–03 and was named the club's player of the season. In June, after 234 league matches, he left for Olympiacos CFP, signing a two-year contract. He was signed to replace Zé Elias at Olympiacos.