Evan Mawarire previously fled Zimbabwe after organising the stay-at-home protests last year under hashtag #thisflag, which was protesting against what some see as President Mugabe's dictatorial, authoritarian government.
He was previously arrested and charged last year with inciting public violence before fresh charges of attempting to overthrow a constitutionally-elected government were then brought during his court trial.
It was then thrown out, after the judge ruled he was not receiving a fair trial.
The church pastor then fled Zimbabwe but returned on Wednesday, where he has now been charged again with subverting a constitutionally-elected government, which carries up to 20 years in prison.
The charges relate to his role in organising peaceful protests against Robert Mugabe in New York during the UN general assembly last year in September.
Muleya Mwananyanda, Amnesty International's deputy regional director for southern Africa, has called the latest charge against Evan Mawarire "absolutely ridiculous and a total sham", saying it was meant to "punish him for speaking out about the declining human-rights situation" in Zimbabwe.
