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2009–2014: Founding and time in lower leagues

On 1 November 2009, Egyptian football management company Masr for Football SAE announced the establishment of the club, with the aim of becoming a leading football club in Egypt concentrating on the youth system. As the 2009–10 season in Egyptian football had already started before November, the club couldn't participate in the lowest league in the Egyptian football league system and was available to enter the Egyptian Fourth Division from the next season. However, FC Masr registered for the league for the 2011–12 season, almost two years after the club was officially founded. Since the Egyptian Fourth Division is a regional league, FC Masr were placed into a group for teams from Cairo.

FC Masr enjoyed a good start to their first-ever season and were close to secure a place in the promotion play-offs, however all football related activities in Egypt were suspended (later abandoned) by the Egyptian Football Association after the Port Said Stadium riot occurred in February 2012 following a 2011–12 Egyptian Premier League match between Al Masry and Al Ahly, which resulted in the death of 74 attendants. In the following season, the club competed in the same group and again finished first, earning themselves this time an immediate promotion to the Egyptian Third Division.

In the Third Division, and similar to the lowest league, FC Masr entered a group for teams from Cairo, Giza, El Monufia and other nearby governorates. The club qualified to the next round of the league, known as the Promotion Groups where teams are divided into groups of 6 teams per group, after leading their regional group. In the Promotion Groups, they succeeded in earning promotion to the Egyptian Second Division for the first time in their history; earning back-to-back promotions from the lowest league to the second-tier league in the league system in only two years.

In November 2020, the club was renamed to ZED FC after the club was purchased by ZED Sports. The new ownership structure implemented former captain Osama Nabieh as manager.

ZED FC's academy won the "Best Academy in Africa" award at the 2021 Globe Soccer Awards.

In December 2021, the club announced a partnership with English Premier League club Aston Villa (which is part-owned by ZED FC owner Naguib Sawiris' brother Nassef Sawiris) to allow young players from their academy to play in Europe. In April 2023, this partnership was expanded and formalised as ZED FC became part of a three-way collaboration with Aston Villa and another part of Nassef Sawiris' V Sports group, Portuguese Primeira Liga club Vitória. The partnership was further expanded in October 2023 with the addition of Japanese J1 League club Vissel Kobe.