Cisse, a former captain of the national team and Paris Saint-Germain player, took over as coach in 2015 and led the country to their first AFCON title two years ago.
Senegal also reached the last 16 of the 2022 World Cup but fell at the same stage of this year’s AFCON, where they were eliminated by hosts and eventual champions Ivory Coast.
The Senegalese FA said an interim coaching team would replace the 48-year-old Cisse for the two 2025 AFCON qualifiers against Malawi this month.
Senegal is level with Burkina Faso on four points from two games in a group that also includes Burundi.
They are also unbeaten in 2026 World Cup qualifying but trail group leaders Sudan by two points after four matches.
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