Trump, during his presidential campaign last year, had called for Gulf states to pay for establishing safe zones to protect Syrian refugees.
A statement after the phone call said the two leaders agreed on the importance of strengthening joint efforts to fight the spread of Islamic State militants.
"The president requested, and the King agreed, to support safe zones in Syria and Yemen, as well as supporting other ideas to help the many refugees who are displaced by the ongoing conflicts," the statement said.
The Saudi Press Agency, in an initial readout of the call, made no specific mention of safe zones, but said the two leaders had affirmed the "depth and durability of the strategic relationship" between the two countries.
The agency later said "the custodian of the Two Holy Mosques had confirmed his support and backing for setting up safe zones in Syria", but did not mention Yemen, where a Saudi alliance is fighting against the Iran-aligned Houthi group.
A senior Saudi source told Reuters the two leaders spoke for more than an hour by telephone and agreed to step up counter-terrorism and military cooperation and enhance economic cooperation.
But the source had no word on whether the two leaders discussed Trump's order to put a four-month hold on allowing refugees into the United States and temporarily ban travelers from Syria and six other Muslim-majority countries.
The source said Saudi Arabia would enhance its participation in the U.S.-led coalition fighting to oust Islamic State from its strongholds in Iraq and Syria.
The White House statement said the two leaders also agreed on the need to address "Iran's destabilizing regional activities." SPA confirmed the report but made no specific mention of Iran.
Both countries share views about Iranian policies in the region, the Saudi source said, suggesting Trump agreed with Riyadh's suspicion of what it sees as Tehran's growing influence in the Arab world. Iran denies it meddles in Arab countries.
The White House statement said the two also discussed what it called an invitation from the king for Trump "to lead a Middle East effort to defeat terrorism and to help build a new future, economically and socially," for Saudi Arabia and the region.
The two also discussed the Muslim Brotherhood, the senior Saudi source said, adding in a reference to the late al Qaeda leader, "it was mentioned that Osama bin Laden was recruited at an early stage" by the organization.