Trump spoke to Egyptian President Abdel Fattah al-Sisi after the attack in Helwan left at least eight dead, as well as a police officer.
The gunman opened fire outside the Saint Mina Coptic church in the district of Helwan, in the latest attack targeting the majority country’s embattled Christian minority.
Trump “condemned the attack and reiterated that the United States will continue to stand with Egypt in the face of terrorism”, the White House said in a statement.
“President Trump emphasised his commitment to strengthening efforts to defeat terrorism and extremism in all their forms.”
Trump has promised to make protecting beleaguered Christian communities overseas a priority for his administration.
The Islamic State group claimed responsibility for the attack.
Footage posted on social media appeared to show the bearded gunman wearing a bulky ammunition vest sprawled on a street, barely conscious, as people restrained his arms and then handcuffed him.
In a statement released via its propaganda agency Amaq, IS said a group of its “soldiers” had carried out the attack, killing 10 “crusaders” and police officers.
It added that one of its fighters had been killed.
An IS affiliate in Egypt has killed dozens of Christians in church bombings and shootings during the past year, and has threatened further attacks against the minority.
The country has been under a state of emergency since April after suicide bombings struck two Coptic Christian churches on Palm Sunday in an attack that was claimed by the local IS affiliate and left over a hundred dead.
Friday’s attack came ahead of Christmas for the Copts, who celebrate it on 7 January.
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