Evan Mawarire was arrested accused of inciting violence but a judge later ordered him to be charged with "plotting to bring down an entire government" - a crime that can mean two decades behind bars.
He was released late on Wednesday after a court in Harare agreed he was not being given a fair trial.
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.
Pastor Evan Mawarire's friend Tauri Nashe Manonge spoke to Premier's Aaron James on the News Hour: