Evan Mawarire had been organising "stay at home" protests to try and shut down the Zimbabwe economy, forcing Mugabe to go.
He had called for a similar mass walk out of workers this week.
In recent months Zimbabwe's civil servants have not been paid and the economic crisis in the country has deepened.
Pastor Evan Mawarire is being charged with section 36 for inciting public violence and disturbing peace. #ThisFlag pic.twitter.com/peCIdIF8Iu
— #ThisFlag (@ThisFlag1980) July 12, 2016
There are food shortages and increasing resentment of President Mugabe, who has been in control since 1987.
Pastor Mawarire attended a police station for questioning this morning where he was then arrested by CID officers.
His official Twitter account said: "Pastor Evan Mawarire is being charged with section 36 for inciting public violence and disturbing peace."
A video is also posted in which he says: "You are watching this video because I have either been arrested or have been abducted. It's a video we had pre-recorded for a day like this one.
"Hold this government to account. Never let them get away with anything.
"Remember this flag is our flag, no-one else loves Zimbabwe more than a Zimbabwean."
In his hands are his 2 weapons, his Bible and his flag. Chete. #ThisFlag @PastorEvanLive @263Chat @ThisFlag1980 pic.twitter.com/NS2bWcKgXi
— Tutsie Kay (@tutsiek) July 12, 2016