The attack prompted Egypt to unleash air strikes on jihadist camps in Libya.
He said the attacks on Christians were aimed at driving a wedge between them and the country's Muslim majority.
Trump, attending the G-7 meeting in Sicily, said the US would stand with Egyptian President Abdel-Fattah el-Sissi, who vowed to strike back at the training bases of Islamic State militants suspected of waging the attacks.
Authorities had previously said 28 were killed in the ambush.
Ten assailants wearing fatigues and face masks fired on the passengers from three four-wheel drive vehicles, Egypt's Interior Ministry told CNN. El-Sisi also appealed to US President Donald Trump to lead the global war against terror.
"Wherever innocent blood is spilled, a wound is inflicted upon humanity", Trump said in a statement.
Persecution of Egypt's Christians has spiked since the toppling of Hosni Mubarak's regime in 2011, and as an ISIS affiliate wages an insurgency on Egypt's Sinai Peninsula.
Trump added that the attack "steels our resolve to bring nations together for the righteous goal of crushing the evil organization of terror, and exposing their depraved, twisted and thuggish ideology".
The attack prompted retaliatory air strikes on jihadists in neighbouring Libya, where ISIS is believe to have trained its fighters.
Egypt has repeatedly expressed concern over militants crossing from Libya to carry out attacks. The terrorist group Ansar al-Sharia, which had recently changed allegiance from al-Qaeda to ISIS, released a video showing the beheading of 21 Egyptian Coptic Christian workers who had been kidnapped while serving as guest workers in Sirte.
Last month, on Palm Sunday, a total of 44 were killed and more than 100 injured in attacks on two churches, one in Alexandria and one in Tanta.