Mr Trump said the Egyptian President, who led a military coup to oust his predecessor in 2013, had done a "fantastic job" and declared his support for Egypt and the Egyptian people.
He also said he had was "very much behind" Mr Sisi and been very close to him since the first time they met.
Mr Sisi told Mr Trump he had a deep appreciation for his "unique personality" and called him "your excellency" three times.
He also vowed to work with the US to eradicate the "evil ideology" that is "terrorising communities."
During the meeting, Mr Trump noted the US plans to build its military to "possibly" its highest levels as it looks to fight Isis and lend support to its allies.
"I just want to let everybody know in case there was any doubt that we are very much behind President Sisi," Mr Trump said.
"He's done a fantastic job in a very difficult situation. We are very much behind Egypt and the people of Egypt."
After no handshake with Merkel, President Trump brushes human rights concerns for not one but two handshakes with Egypt's leader el-Sisi pic.twitter.com/32uOqNpJvz— Bradd Jaffy (@BraddJaffy) April 3, 2017
While Mr Trump noted the US and Egypt "have a few things" they do not agree on, he did not air US concerns about human rights in Egypt.
"I just want to say to, Mr President, that you have a great friend and ally in the United States, and in me," Mr Trump said.
Human rights groups have estimated that Mr Sisi's government has detained at least 40,000 political prisoners.
Mr Trump has repeatedly mentioned Egypt as a critical Muslim-majority ally in the fight against extremists such as Isis.
The White House welcome comes after a tense relationship between Egypt's leader and the previous administration.
Former President Barack Obama never invited Mr Sisi to the White House and allowed his administration to repeatedly admonish his government over its human rights record.
He froze aid to Egypt for two years after Mr Sisi, then a general, overthrew President Mohamed Mursi in mid-2013 after mass protests against his rule. Mr Mursi, a Muslim Brotherhood member, had been elected the previous year.