The Pharaohs will also play both sides in the 2018 Fifa World Cup qualifiers.
The North Africans have already faced Ghana in the first leg of the World Cup qualifying in November, picking up a 2-0 home victory.
“I wasn’t happy to know that we’re going to face Ghana and Uganda again in the Afcon," Cuper was reported as saying by Kingfut.
"I wanted new competitors, but I shifted my thinking to something more positive.
“In football, you have to be ready to face obstacles.
"I have no previous experience of Afcon and I have never played in short-timed competitions.
"However, we’re deeply concentrated and have high hopes.
Before taking on Uganda and Ghana, the Pharaohs will open their Afcon campaign against Mali on Tuesday.
Cuper continued: “Right now, we’re only thinking about our match against Mali.
"We’ll [take a] step at a time."
Egypt are seven-time winners of the Afcon, and are set to make a return to the championship following a seven-year absence.