Addressing a ceremony Sunday evening at Cairo's Qubba presidential palace, Sisi said he is looking forward to "reconciliation with all citizens but except those committed crimes against the nation or using violence as a methodology".
Sisi, who led the ouster of former Islamist leader Mohamed Morsi July last year, won almost 97 percent of the votes in the last week's presidential election, Xinhua reported.
Morsi's Islamist supporters led by the currently-blacklisted Muslim Brotherhood claim the move was as a "military coup".
Sisi said he would work for a comprehensive development, combating terrorism and improving security.
However, some worried that Sisi's rule will be reproduction of former regime of Hosni Mubarak that was characterised by repression and police brutality.
The 59-year-old said he will work hard to create "a healthy relation between security apparatuses and the people based on preserving dignity and respecting freedom." Yet he warned that "freedom without commitment leads to disorder".
About 1,200 diplomats, including outgoing President Adly Mansour, cabinet members as well as local and foreign dignitaries, showed up at the palace ceremony.
On Sunday morning, Sisi was sworn-in at the Supreme Constitutional Court in Cairo as Egypt's new president amid massive security presence. The military strongman comes to office nearly one year after the ouster of his predecessor.