"Following his re-election, we look forward to continuing to work with President Abdel fattah al-Sisi to advance our strategic partnership and address our common challenges", Nauert said.
Sisi won the second four-year term garnering more than 97 per cent votes, according to official results announced on Monday by the election commission.
It's the same proportion that the former military commander secured four years ago for his first term but with a lower turnout, official results showed on Monday.
In an interview days ahead of the vote, Sisi said he wished there were more candidates, denying any role in sidelining his rivals.
One day later, another serious contender, rights lawyer Khaled Ali withdrew, saying he and his supporters were being intimidated.
Voter turnout was 41 percent in the March polls, National Election Authority head Lasheen Ibrahim told a news conference in Cairo. Turnout in the 2014 vote was 47 percent. His sole challenger, the little-known centrist politician and al Ghad party chief, Moussa Mostafa Moussa won 2.92 per cent of valid votes.
State media portrayed failure to vote as a betrayal of Egypt.
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El-Sissi began his rule after leading a military coup in 2013 against then-President Mohamed Morsi. Mr Sisi swept to victory in an election a year later with 97 percent of the vote.
In a call to Mr Sisi on Monday, US President Donald Trump expressed his "sincere congratulations" and said the United States was keen on strengthening strategic relations, according to Egyptian state news agency MENA.
Trump's decision to congratulate the fellow president could face criticism.
"I promise that I will remain faithful to my pledge with you, to be honest in my work for the sake of the greatness of our great homeland, and to build up its institutions with all the strength and determination I have and to achieve development and stability", President Sisi said in a televised speech.
Trump has repeatedly bucked Washington norms since coming to office, congratulating foreign leaders on elections that his own officials say were dubious, unfair or rigged.
"It hopes that his reelection will allow him to satisfy the legitimate aspirations of the Egyptian people for security, prosperity and the full expression of freedoms in a constitutional framework", she said without elaborating.