The Cranes qualified for the knockout stage of the biennial tournament for the first time since 1978 with a 2-0 victory over the Democratic Republic of Congo, a 1-1 draw with Zimbabwe before losing 2-0 to Egypt to finish with four points behind the Pharaohs in Group A.
Senegal have met with Uganda five times previously, with the Terenga Lions winning two of the meetings while three ended in draws including their last encounter in June 2017.
Cisse has warned his side to be battle-ready for a difficult game against the Cranes as any slight mistakes could lead to their exit from the tournament.
“Now it’s direct elimination, it will be hard, the Ugandan team are the team who have lost the least in the last few years,” Cisse told Goal.
"We played a friendly before the World Cup, we had a 0-0 draw and everyone said they were a little team, that we should have won, and I said be careful - this is a team who are progressing.
“They kept their identity African, they play like true Africans, you have to respect this.”
Senegal last won a game in the knockout stage of the Africa Cup of Nations in 2006, coming in their quarter-final match against Guinea.
They will hope to end the unfavourable record when they slug it out with the Cranes at the Cairo International Stadium.