Mr Brunson has been in a Turkish jail since October 2016 for allegedly being a threat to national security.
Turkey suspect the pastor has ties to the organisers of the 2016 coup in July to try to oust President Recep Tayyip Erdogan.
Angry at the US citizen’s detention, Trump tweeted: “A total disgrace that Turkey will not release a respected U.S. Pastor, Andrew Brunson, from prison.”
US media has said how the Pastor and his wife were in charge of a ministry in the coastal town of Izmir.
They were said to be there for nearly 20 years.
Andrew Brunson is not the only person to have been detained since the failed coup.
Thousands have been held in custody accused of having links to the US-based cleric Fethulla Gelen.
Trump tweeted after a Turkish court denied a request for the release of Andrew Brunson.
The 50-year-old pastor is originally from Black Mountain in North Carolina.
He faced up to 35 years in prison for “committing crimes on behalf of terror groups without being a member and espionage”.
Evidence in court was provided by two people who have not been named.
Some US politicians have questioned whether there needs to be sanctions against Turkey if he is not released.
His case is said to have been discussed by Trump and President Erdogan over the phone.
State Department spokeswoman Heather Nauert said: “We believe he is innocent.”
She added: “We continue to call on the Turkish government to quickly resolve this case in a timely and transparent and fair manner.”
Mr Brunson has been quoted telling the court: “I believe in and support Turkey’s territorial integrity.
“I forgive those who lie and bear false witness against me.”