Papaioannou started his football career at Rodos with which he made great appearances, attracting the interest of the big clubs.
On 9 July 1983, he was transferred to AEK Athens for 10 million drachmas plus the incomes from a friendly match between the two club in Rhodes.
He stood out for his good physical condition, his continuous running and his contribution mainly in the blocking part, while also participating in the offensive.
The most important moment in his career was his goal against Real Madrid in the 1–0 win for the UEFA Cup that took place at 18 September 1985.
He left AEK in the summer of 1993 when the management decided to proceed in a small renewal of the roster and moved to Kalamata for a season.