With the outcome of the election a foregone conclusion, authorities went to great lengths to boost turnout, using their vast resources to get voters out and threatening on the third and final day of the election to fine anyone boycotting the vote.
Sisi ran virtually unchallenged after the other serious candidates were arrested or pulled out.
Turnout of 47 percent in that year's election was sharply higher than this year's 41 percent despite appeals from Prime Minister Sherif Ismail for voters to fulfil their patriotic duty.
Sisi won a total of 21.8 million votes compared with 656,534 for his opponent, Moussa Mostafa Moussa, whose tally was less than the 1.8 million spoiled ballots.
His tenure was renewed officially on Monday after he was declared president for a second term till 2022 upon securing 97.07 percent of valid votes, winning against sole competitor Moussa Moustafa Moussa in an expected sweeping win.
Voter turn out was a low 41 per cent, with the United Nations and worldwide observers expressing concern over the government's crackdown on dissent.
The elected President would take the following oath before the People's Assembly: "I swear by Almighty God to uphold the Republican system with loyalty, to respect the Constitution and the law, and to look after the interests of the people fully and to safeguard the independence and territorial integrity of the motherland".
Trump said in the call that the United States was keen on strengthening strategic relations and continuing to coordinate on key issues, MENA reported. "Egypt has an opportunity over next 4 years to build a prosperous & democratic society, building on rights set out in 2014 constitution".
But Nauert added: "We have noted reports of constraints on freedoms of expression and association in the run-up to the elections".