The two leaders spoke on the phone Sunday evening about the attack that was carried out by a Saudi military trainee.
"The Crown Prince reiterated Saudi Arabia’s commitment to working with the United States to prevent a horrific attack like the Pensacola shooting from ever happening again," the White House said in a statement, adding that Trump thanked the Crown Prince for his assistance and "continued partnership".
The FBI officially identified the shooter who killed three people as Mohammed Alshamrani, a 21-year-old second lieutenant in the Royal Saudi Air Force who was a student naval flight officer at the Naval Aviation Schools Command at Naval Air Station Pensacola.
FBI officials said the investigation in the incident was taking place under the "presumption" it was an act of terrorism, but that the gunman had likely acted alone.
FBI Investigating Shooting at US Naval Base as Terrorism
A Saudi national, who was a foreign flight student at the Florida base, has been identified as the shooter responsible for the deaths of 3 people
Authorities are still searching for a motive for the rampage which also injured eight others.
The shooter, who was also killed in the incident, is reported to have hosted a dinner party earlier in the week where he showed videos of mass U.S. shootings to his guests, according to media reports. At least one of his guests is reported to have videotaped Friday's massacre. Several Saudi students are being held for questioning.
U.S. Defense Secretary Mark Esper said Sunday that he has instructed the armed forces to review their screening processes of foreign soldiers and security on military installations following the deadly shooting.
The victims were also students at the flight school. They have been identified as Ensign Joshua Kaleb Watson, 23, from Coffee, Alabama; Airman Mohammed Sameh Haitham, 19, from St. Petersburg, Florida; and Airman Apprentice Cameron Scott Walters, 21, from Richmond Hill, Georgia.