Andrew Brunson, who ran a Protestant church in the western city of Izmir, has been detained by Turkish authorities since October 2016. If convicted, he risks up to 35 years in jail.
"Pastor Andrew Brunson, a fine gentleman and Christian leader in the United States, is on trial and being persecuted in Turkey for no reason," Trump tweeted late Tuesday.
"They call him a Spy, but I am more a Spy than he is. Hopefully he will be allowed to come home to his beautiful family where he belongs!"
A Turkish court ruled Monday to keep Brunson in custody, deeming him to be a flight risk.
He is accused of engaging in activities on behalf of the group led by exiled Muslim preacher Fethullah Gulen -- who Ankara says is behind a failed 2016 coup -- and the Kurdistan Workers' Party (PKK).
Both the Gulen movement and the PKK are banned by Turkey as terror groups.
Brunson is also accused of espionage for political or military purposes.
In an indication of the importance of the case for Washington, his hearing on Monday was attended by Sam Brownback, the US ambassador at large for religious freedom, and Senator Thom Tillis from Brunson's home state of North Carolina.
The US State Department meanwhile said it had seen "no credible evidence" Brunson was guilty of a crime.
The Brunson case has further hiked tensions between NATO allies Turkey and the United States, with US President Donald Trump raising the issue in talks with Turkish counterpart Recep Tayyip Erdogan.
Relations are already strained over American backing for a Kurdish militia in Syria despised by Ankara and the jailing of two employees at American missions in Turkey.