Greeting Sisi warmly in the Oval Office, Trump heaped praise on the former general's leadership and unleashed a charm offensive designed to mend ties strained by crackdowns, revolution and revolt.
"You have a great friend and ally in the United States and in me," Trump told Sisi, sweeping aside his predecessor Barack Obama's concerns about the Sisi government's purge of political opponents and rights activists.
"I just want to let everybody know that we are very much behind President al-Sisi - he has done a fantastic job in a very difficult situation," Trump said.
The meeting symbolizes the Egyptian leader coming in from the cold, after years of being kept at arm's length by Washington.
The last time an Egyptian president was at the White House was in 2010, when Hosni Mubarak attended Middle East peace talks alongside Israeli, Palestinian and Jordanian leaders.
Within months, Mubarak was ousted by a popular uprising, as the Arab Spring swept across the region.
The revolt gained tacit support from Obama, who warned the military against quashing protests by force.
In the months and years that followed, the Egypt-US relationship was strained further as a broadly Islamist and then a military government - led by Sisi - took charge.
The Obama administration temporarily froze military aid to Egypt - worth roughly a billion dollars a year - after then-defence minister Sisi led the 2013 coup against president Mohamed Morsi, and a bloody crackdown on his supporters.
Egypt's key role as the most populous Arab nation meant that aid was fully reinstated in 2015, but diplomatic relations remained difficult.
The catalyst for Trump and Sisi's friendship has been a common hardline stance against jihadist groups, which Sisi described as "a satanic ideology" during brief remarks at the White House.
The former New York property tycoon and the former Egyptian army general, who do not plan to hold a joint press conference, previously met in September when Trump's campaign was still in full swing.
Trump at the time called Sisi a "fantastic guy."
Sisi was reportedly the first to call Trump to offer his congratulations on his November election win.
In one of several public appearances on Monday, Trump said "we have many things in common, We have a few things that we don't agree on."
"I think that this is going to be a very productive day," he said.
Asked directly whether human rights were discussed, Trump declined to answer.
At the top of Sisi's priorities during the meeting will be convincing Washington to designate the Muslim Brotherhood a "terrorist group", an Egyptian diplomatic source told The New Arab.
Egyptian lawmakers accompanying Sisi on the week-long trip are lobbying Congress to classify the blacklisted group as a terrorist organisation, Egyptian state media reported.
The Muslim Brotherhood won several democratic elections in 2011 and 2012, only to be removed from power by force as part of the military coup led by Sisi.
The group has been declared a "terrorist group" in Egypt and have been repeatedly blamed for acts of violent extremism.
The Trump administration, however, seem to have reservations about following suit with Sisi's wishes.
"The President is interested in hearing President Sisi’s views on the Muslim Brotherhood issue… We, along with a number of countries, have some concerns about various activities that the Muslim Brotherhood has conducted in the region," a senior White House official told reporters on Friday.
The Egyptian diplomat, who spoke on the condition of anonymity, said that the Syrian conflict would not be a major focus of the meeting because the Trump administration does not think Egypt is a main player in the crisis.
"Libya will be one of the main issues discussed. Sisi will present a plan for a new Libyan government with a special place politically and militarily for his ally General Khalifa Haftar," the source said.
Rights groups slammed Trump for meeting with Sisi, whose regime has killed and imprisoned thousands of people since coming to power.
"Inviting Sisi for an official visit to Washington as tens of thousands of Egyptians rot in jail and when torture is again the order of the day is a strange way to build a stable strategic relationship," said Sarah Margon, Washington director at Human Rights Watch.
Dozens of activists staged a silent protest on Sunday near the Washington Monument against the meeting.
Agencies contributed to this report.
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