"Human rights are not a constraint but also a way to fight against terrorism," said Hollande at a press conference with Sisi.
Before he arrived in Cairo rights group Amnesty International slammed France's "deafening silence" on allegations of repression and abuses in Egypt.
"The region we live in, President Hollande, is very turbulent," Sisi replied, adding that "European criteria" of human rights should not be applied to a country struggling with "an evil force" that is spreading a "false impression" of what is happening there.
Italy recently recalled its ambassador to Egypt for consultations following the murder of Italian doctoral student Giulio Regeni, whose body was found covered in torture marks in February in Cairo more than a week after he disappeared.
Hollande said he raised Regeni's case and that of Eric Lang, a French teacher who was murdered in an Egyptian jail in 2013, during his meeting with SIsi.
He said he intends to provide a list of personal cases of rights violations.
Although the European parliament has passed a motion demanding a halt to all military cooperation with Cairo, Hollande was due to sign deals worth 1.1 billion euros in arms sales, including fighter jets, military communications systems and navy vessels, making France Cairo's largest weapons supplier.