President Barack Obama will speak with the former army chief in the coming days, the White House said in a statement.
Washington looked forward to working with Sisi "to advance our strategic partnership and the many interests shared by the United States and Egypt," it said.
The statement added: "We urge the President-elect and the government to adopt the reforms that are needed to govern with accountability and transparency, ensure justice for every individual, and demonstrate a commitment to the protection of the universal rights of all Egyptians."
Sisi took a sweeping 96.9 per cent of the vote in elections last week held nearly a year after he toppled president Mohamed Morsi, whose Islamist allies boycotted the polls.
With an economy hammered by years of unrest, Sisi today urged Egyptians to "work to return security to this nation," in a television address after the final results were declared.
"The future is a blank page, and it is in our hands to fill with what we want ... bread, freedom, human dignity, social justice," he said.
Sisi's appeal mirrored the slogan of the 2011 uprising that overthrew dictator Hosni Mubarak, as Sisi's critics warned the retired field marshal could impose an even more repressive government.
Morsi's Muslim Brotherhood, crushed by a massive crackdown following his overthrow and detention, had boycotted the vote.
At least 1,400 people, mostly Islamists, have been killed in street clashes with police, and more than 15,000 people have been arrested.
The crackdown has extended to secular dissidents who spearheaded the uprising against Mubarak, with several of their leaders imprisoned for holding protests against the army-installed government after Morsi's ouster.
The United States firmly refrained from calling the change of government that saw Morsi deposed a coup. That assessment would have forced it under US law to stop providing Egypt with billions in annual aid.
In the statement, the White House said observers found the elections were held in accordance with Egyptian law.
But it also expressed concern about what it called the "restrictive political environment" in which the vote took place and urged Sisi's new government to step up rights reforms.
"We have consistently expressed our concerns about limits on freedom of peaceful assembly, association, and expression and call upon the government to ensure these freedoms as well as due process rights for all Egyptians," it said.