The 31-year-old had reportedly been in conflict with the club's board, resulting in his exit, though he remains keen to remain a part of the Egyptian giants in another capacity
The 31-year-old replaced Helmy Toulan in January and guided them to the play-off stage of the domestic league, while retaining the Egyptian Cup with victory over Smouha.
Despite that relative success, Mido has lasted just seven months in the dugout following reports of several disputes with the club's board, though the former striker is keen on staying on in another capacity.
He told the press: "Ahmed Suliman of the board of directors has told me of their decision to dismiss me.
"I'm still the son of Zamalek and I am ready to serve them in any capacity."
Mido retired from playing aged just 30 in June 2013, having played for 12 different clubs, including Zamalek, Ajax, Marseille, Roma and Tottenham, before an ill-fated spell at Barnsley saw him hang up his boots.