Evan Mawarire emerged as the leader of the popular #ThisFlag protest movement that quickly grew into the largest street demonstrations against Mugabe in several years.
"Unfortunately I have been arrested again," Mawarire said in a Facebook video posted while in handcuffs at the Harare central police station.
"I hope we will get through this... But this is home to me, I am allowed to come back home. I committed no crime."
The police were not immediately available to comment.
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At the airport, Mawarire "was escorted into another room by three men even before he went through immigration or customs", his sister Telda told AFP.
The pastor fled to South Africa in July and then to the United States in fear for his life after being publicly denounced by Mugabe, whose ruthless security forces crushed the protest movement using batons, tear gas and water cannon.
The cash-strapped government has struggled to pay civil servants and the military on time as the economy has suffered a severe meltdown with more than 90 percent unemployment.
The 92-year-old Mugabe, who is increasingly frail, has vowed to stand for re-election in 2018, though ZANU-PF party seniors have long been jockeying to step into the role when he dies.
The national flag became a symbol of anti-government protests after Mawarire, a little-known evangelical pastor, posted a Facebook video last April in which he had the flag wound around his neck as he deplored the country's worsening economic crisis.
He added that he was considering running for public office in Zimbabwe, where Mugabe has dominated politics since national independence in 1980 through election rigging and violence.
In a vote widely seen as not credible, Mugabe easily defeated the opposition Movement for Democratic Change (MDC) party in the last election in 2013.
Vice President Emmerson Mnangagwa is viewed as the most likely next leader, with Mugabe's wife Grace, 51, also a possible candidate.