The former army chief took the oath of office at the Constitutional Court in a suburb south of the Egyptian capital Cairo, the same venue where Mohamed Morsi, the president who he deposed, was sworn in two years ago.
Sisi is the fifth Egyptian president to come from the army's ranks. The ceremony also marked the first time one president handed power to the next, although Adly Mansour, the former interim president, was appointed by Sisi.
Sunday was declared a national holiday and tight security was enforced by the police and military throughout Cairo.
"Cairo has announced a state of emergency across its institutions, and no breaks will be taken today and on Sunday," Ahmed Sakr, the deputy governor of Cairo, said on Saturday.
Sisi was declared the country's president last week after ‘winning’ 96.6 percent of the presidential vote, ‘beating’ the only other contender, Hamdeen Sabahi, who won 3.09 percent.
Several regional heads of state were among those who attended the ceremony.
Asraf Abdul Ghaffar, a senior member of the Brotherhood, told Al Jazeera that he believed many in Egypt did not recognize Sisi's presidency.
"Sisi is not the president. Morsi has not resigned. The legitimate president is Mohamed Morsi," he said. "Sisi has cracked the Egyptian community."
PHOTO CAPTION
Abdel Fattah al-Sisi (C) and interim head of state Adly Mansour (C left) pose for a group picture with constitutional court members after Sisi swore in as President in Cairo June 8, 2014 in this handout provided by The Egyptian Presidency.
Al-Jazeera