Evan Mawarire was arrested accused of inciting violence but a judge has ordered him to be charged with "plotting to bring down an entire government" - a crime that can mean two decades behind bars.
He has been organising "stay at home" protests to try and shut down the Zimbabwe economy, forcing the president to step down.
Pastor Mawarire, 39, had called for a similar mass walk out of workers this week using the hashtag #thisflag on Twitter.
In recent months Zimbabwe's civil servants have not been paid and the economic crisis in the country has deepened.
Robert Mugabe, 92, has led the country since independence in 1980 with many arguing he has brought the country to its knees.
Protestors gathered outside the court in the capital Harare as Pastor Mawarire arrived for his hearing. Many sat praying as riot police armed with water cannon and tear gas looked on.
#FreePastorEvan shocking..state opposes bail says its a serious crime & defense counsel shld approach the high court pic.twitter.com/z0ieqsj9i5
— Jabusile Shumba (@JabuShumba) July 13, 2016
A judge denied Pastor Mawarire bail and ordered him to be held in custody until trial.
A spokesman for the Zimbabwe government warned anyone demonstrating against President Robert Mugabe would face the "full wrath of the law".
Amnesty International's Southern Africa Deputy Director Muleya Mwananyanda said: "The arrest of Pastor Evan Mawarire appears to be a well-calculated plan to intimidate him and other activists ahead of the national shutdown organised for tomorrow in an attempt to supress the rights to freedom of expression and peaceful assembly.
"Instead of suppressing dissenting voices, Zimbabwean authorities should be listening to protesters like Evan Mawarire.
"They have a right under Zimbabwe's constitution and international treaties ratified by Zimbabwe to express themselves, peacefully protest and defend their rights."