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.
Sisi took a sweeping 96.9 percent of the vote in an election held nearly a year after he toppled president Mohamed Morsi, whose Islamist allies boycotted the polls.
The United States firmly refrained from calling the change of government 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.
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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.
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."
As Egypt looks ahead to parliamentary elections later this year, Washington urged the country to consider ways to improve how future elections are held.
"True democracy is built on a foundation of rule of law, civil liberties, and open political discourse," the statement said.