At the White House, the two sides on Friday signed the so-called "safe third country" agreement, requiring migrants who pass through Guatemala to seek asylum there rather than heading to the US, Xinhua reported.
Witnessing the signing ceremony, Trump told reporters that the pact will put "coyotes and the smugglers out of business."
Trump has long been criticizing the so-called Northern Triangle countries of Central America, namely Guatemala, El Salvador and Honduras, accusing them of having not done enough to prevent their citizens from leaving to seek asylum in the United States and has tried to cut aid to them as punishment.
Under the deal, asylum seekers from Honduras and El Salvador, who have to traverse Guatemala on their way up to the US, will be directed to seek protection there.
The deal came days after Trump on Tuesday threatened to impose tariffs and other penalties on Guatemala, after the Central American nation's high court blocked its government from signing an asylum deal with Washington.
Earlier this month, Guatemala's high court ruled that Guatemalan President Jimmy Morales could not commit to the deal with the US side without the approval of the nation's parliament.
It was still unclear how Morales will implement the agreement, given the Guatemala's court ruling.
The White House has been tough on immigration, an issue expected to be widely discussed in the days leading up to the 2020 presidential election.
( With inputs from IANS )