Cuper quits as Aris coach
The 55-year-old former Inter Milan and Valencia manager signed a new contract with Aris last year after leading them to the Greek Cup final which they lost to Panathinaikos.
He led his team into the last 32 of the Europa League but they have struggled for consistency domestically, lying eighth in the 16-team standings.
"Aris announces the resignation of coach Hector Raul Cuper from the technical leadership of the team," a club statement said.
Cuper thanked the club for their support.
"After recent bad results, the best thing for the team is for me to leave," he said.
"My decision is irrevocable despite persistent pressure and effort from the club's administration to persuade me to stay. I wish every success to Aris in achieving its objectives."
Cuper coached Valencia from 1999-2001 and guided the Spanish side to successive Champions League finals in 2000 and 2001.