Trump, speaking to reporters at the top of the meeting, did not mention human rights as a topic for discussion despite concerns from some advocacy groups that Egypt is stifling dissent before a planned constitutional referendum that would potentially allow el-Sissi to remain in power until 2034.
Trump instead praised Egypt's efforts to confront terrorism, saying "a lot of progress had been made in a lot of different ways in terms of terrorism."
Both leaders also said the relationship between the U.S. and Egypt had never been better. They spoke before the meeting. Afterward, cameras showed Trump walking with el-Sissi out of the West Wing and giving him a thumbs-up as he departed.
El-Sissi led the 2013 military overthrow of elected but divisive Islamist President Mohammed Morsi. He has presided over an unprecedented crackdown on dissent, and was re-elected last year after all potentially serious challengers were jailed or pressured to exit the race.
Trump was asked about the referendum effort in Egypt and El-Sissi's bid to stay in power.
"I don't know about the effort," Trump said. "I can just tell you he's doing a great job."
Human Rights Watch said the coming election referendum would constitutionally undermine an already weak judicial independence and increase military control of the public and political spheres.
"Given President Trump's silence on abuses, Congress should step up and condemn this initiative," said Michael Page, deputy Middle East and Northern Africa director at Human Rights Watch.
The group also said Egypt's efforts to stem dissent had led to unfair mass trials, whether before military or civilian judges, for thousands of dissidents. Although many of those verdicts have been overturned, Egyptian authorities have executed at least 180 people since 2013, Human Rights Watch said.
The White House issued a summary of U.S.-Egypt collaboration once the meeting was over. It stated that the Trump administration "encourages the Egyptian government to preserve space for civil society and to protect human rights."