"Al-Gohari thanked all Egyptian FA officials for trusting him during his one-year spell here," the Association said on its official website.
"But he said he won't be able to carry on his duties. The Egyptian FA wishes him the best of luck in future."
Al-Gohari has apparently decided to resign after a disagreement with some Egyptian FA board members over the launching of a new U-23 competition.
The 71-year-old believed the new competition would help some players rediscover their form even if they were out of favor with their teams.
But Al-Gohari, a highly-respected coach who enjoyed a great success while in charge of the Egyptian national team, was frustrated as his plan never came to light.
Ismaili, who are yet to appoint a new coach following the resignation of Emad Soliman, have recently tried to appoint Al-Gohari as their new manager.
But the former Ahli and Zamalek tactician said he was not interested in returning to club management.