Critics, including Republicans and Democrats in Congress, had warned Trump to take a tougher stance on the Egyptian leader, one week before his supporters' majority in parliament is set to approve new constitutional amendments that would expand his control of the judiciary and allow him to remain in office until 2034.
A bipartisan group of 17 senators urged the Trump administration to tell Sisi to reconsider the move, which has been condemned as a dangerous power grab that could foment political unrest even as it bolster's the general-turned-president's rule.
"If Egypt continues in this direction, the future is predictable, and it’s ominous. Rather than becoming a modern, stable, and prosperous country -- which it could -- it will become increasingly divided and unstable," Sen. Patrick Leahy, D-Vt., said Tuesday.
White House officials told reporters Monday that the administration was "obviously... aware of this" move, and it would be part of a "very frank and open" conversation between the two leaders about human rights and civil society.
But President Trump said he didn't know about it on Tuesday when sitting next to Sisi in the Oval Office.
"I don't about the effort, I can just tell you he's doing a great job," Trump said, declining to condemn or urge against it.
As he has on previous occasions, including a 2017 visit to the White House, Trump praised Sisi for his efforts to combat terrorism in Egypt and said the U.S.-Egyptian relationship had never been better. Sisi responded with similarly strong words about the partnership and Trump's leadership.
The White House readout of their meeting also made no mention of human rights or political issues, instead highlighting that they discussed the fighting in neighboring Libya, "the threat posed by the Muslim Brotherhood," water issues and religious freedom -- which Secretary of State Mike Pompeo has praised Sisi for promoting, especially on behalf of Egypt's Christians.
Sisi's government is accused of launching the most aggressive crackdown on political opponents from across the political spectrum in the country's modern history, according to Amnesty International. That especially includes the Muslim Brotherhood, a transnational political party that Sisi's government has declared a terrorist organization after he helped oust his predecessor Mohamed Morsi, a Muslim Brotherhood leader, in a popularly-backed coup in 2013.
While Sisi has repeatedly insisted that there are no political prisoners in Egypt, Human Rights Watch estimated there are currently 60,000 behind bars in Egypt, detained on political grounds.
Pompeo was grilled about that human rights record on Capitol Hill after attending Trump and Sisi's meetings.
"There's no doubt that it's a mean, nasty world out there," the top U.S. diplomat told lawmakers in defense. He added what separated Sisi from the likes of Venezuelan President Nicolas Maduro, whom the Trump administration has tried to push from power, is that Sisi is "actually partnering with us to help keep Americans safe... You might call them [both] tyrant, you might call them authoritarian, but there's a fundamental difference."
Pompeo said he raised human rights issues with Sisi in their own meeting on Monday night, "asking him to do better... certainly with respect to Americans" detained by the Egyptian government. There are approximately 20 U.S. citizens currently imprisoned, including Mustafa Kassem, a New York City taxi driver in severe health because of an ongoing hunger strike.
But that wasn't enough for Democrats in particular, who condemned Trump's cozy relationship with Sisi.
"Whatever may be said on other side of Pennsylvania Avenue today, I think it’s pretty clear the president does not speak for the United States. He does not speak for the United States Congress, certainly, in terms of our perception of what is going on in Egypt," said Rep. Tom Malinowski, D-N.J., who served as President Obama's assistant secretary of state for democracy, human rights, and labor.
ABC News's Randa Ali contributed to this report from Cairo.