Cuper, 62, had been in charge of Egypt since 2015 and led them to the final of the 2017 Africa Cup of Nations, where they fell to Cameroon.
However, the former Inter manager's biggest achievement was securing their first FIFA World Cup appearance since 1990 - which brought about major optimism with Liverpool superstar Mohamed Salah leading their attack.
However, Salah's well-documented shoulder injury problem and political controversy shrouded their historic feat as they exited Russia 2018 without a victory in Group A.
The Pharoes have since released a statement regarding Cuper's future as their tournament ended abruptly with a 2-1 defeat to Saudi Arabia on Monday.
"We held a meeting after returning from Russia and the entire board decided to say thank you to Cuper and his technical staff," the statement read.
"We appreciate the work from the coach, from reaching the Africa Cup of Nations after three years of absence and taking Egypt to the World Cup after 28 years of absence."