The EFA, which made the announcement in a brief statement, has not clarified whether Essam Abdel-Fattah, the current head of the Egyptian refereeing committee, will keep his job.
Clattenburg is one of the most decorated English referees, having officiated in the elite Premier League for 13 years.
He also took charge of a number of high-profile games in Europe, including the Euro 2016 final and the Champions League final in the same year.
In early 2017, Clattenburg left the Premier League and replaced fellow Englishman Howard Webb as the head of Saudi Arabia's refereeing committee. Two years later, he became a professional referee in China.
Despite the introduction of the Video Assistant Referee (VAR) technology in Egyptian football, the referees have come under fire from the majority of Premier League clubs this season.
Many contentious decisions have dominated headlines, with Cairo giants Ahly repeatedly asking for foreign referees to take charge of their respective games. The EFA said it would allow foreigners to officiate domestic games as long as the concerned club cover all expenses.
This month, Spanish referee Jose Montero officiated a thrilling Cairo derby clash between Ahly and Zamalek that ended in a 2-2 draw, while Romanian Istvan Kovacs took charge of Ahly's 2-1 win over Pyramids FC in the Egypt Cup quarter-final.
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