The Turkish Foreign Ministry confirmed the meeting via social media but did not reveal details about the discussions.
Fidan's visit to Egypt commenced on Sunday, following an invitation from Egyptian Foreign Minister Badr Abdelatty, who was appointed to the role last month.
During his visit, Fidan also stopped by key locations including Egypt's al-Arish port, the Rafah border crossing, and the Egyptian Red Crescent Logistics Center.
In addition to his meeting with President Sisi, Fidan met with North Sinai Governor Major-General Khaled Megawer and Arab League Secretary-General Ahmed Aboul Gheit. (ILKHA)