Papatheodorou played basketball in the Athinaikos youth club systems in Greece, and as soon as he stopped playing youth level basketball, at age 20, he began his coaching career in the same Athinaikos club systems, working there from 1995 to 2001.

He became the assistant coach of the senior men's team for one season, in 2001, in the Greek lower divisions.

After leaving Nea Kifissia, Papatheodorou was appointed as the head coach of the Kazakh NBL and VTB United League club Astana.

[4] On 19 June 2019, Papatheodorou signed a three-year contract with AEK Athens replacing Italian Luca Banchi.

[5] In the summer of 2022, Papatheodorou returned to coaching at a club level and signed with Kolossos Rodou, replacing Ilias Kantzouris.