The Pharaohs suffered a shock exit from the 2019 Africa Cup of Nations following a late defeat to South Africa in the round of 16.
Thembinkosi Lorch's 85th-minute strike cemented victory for the Bafana Bafana at the Cairo International Stadium.
Following the humiliating exit, EFA president Hany Abou-Rida has left his position alongside a number of board members, including Hazem Emam and Ahmed Megahed.
Despite the resignation, Abou-Rida will continue in his position as the head of the organizing committee of the 2019 AFCON.
Aguirre was appointed as Egypt manager in August 2018 and since then he took charge of the Pharaohs in 12 games across all competitions.
During his time in Egypt, the Pharaohs won nine games, drew one, while losing only twice. The national team scored 25 goals under his charge while conceding seven.
His contract which saw him earn a monthly salary of $120,000 was supposed to run until the 2022 World Cup, but a disastrous AFCON campaign saw him depart early.
READ ALSO:
Â