Several months after his retirement, Papadopoulos began his coaching career as an assistant manager at Proodeftiki in the Greek Alpha Ethniki.
Papadopoulos moved to Cyprus and was appointed head coach of Cypriot First Division side Apollon Limassol.
He resigned after three games, and was appointed head coach by fellow Football League side Veria until January 2011.
He left the club in January 2012, and was appointed head coach of Iraklis in the Football League 2 Northern Group.
At the start of the 2012–13 season, in October 2012 and after consecutive bad results during the championship, Papadopoulos resigned as coach of Doxa Drama and was subsequently hired again by Olympiacos Volos, where he stayed until January 2013.
Given the club's financial situation and struggling nature, Papadopoulos successfully managed to stay clear of relegation at the end the season, but terminated his contract in June, only to be re-appointed in December that same year to replace Zoran Milinković.
In July 2014, he took over management of Cretan club Chania in the Football League but was replaced in October that same year.
In August 2015, Papadopoulos was hired by Lamia, departing after a loss against his former club AEL during the opening match of the 2015–16 Football League season.