Mawarire responded “not guilty” when the two charges of subverting a constitutional government and incitement to cause public violence were read to him in the high court in Harare.
The subversion charges carry a 20-year prison sentence.
Judge Priscilla Chigumba granted Mawarire $200 bail, and ordered him to report once a week to police.
He was also ordered to surrender the title deeds of his parent’s property as part of his bail conditions.
The charges stem from his involvement in organising a crippling strike in July last year that shut down major cities and paralysed public transport, prompting the government to ban public protests.
Although Mawarire was granted bail, he has to remain in police custody until he appears before magistrates following his fresh arrest on Sunday in a separate case.
The 40-year-old pastor was taken by police during a church service on Sunday after he posted a video on social media criticising the dire economic conditions in the country.
He is yet to be officially charged.
The video showed long queues at fuel stations, as petrol and diesel supplies had run out in many stations across the capital Harare, in the midst of severe foreign currency shortages.
Zimbabwe is battling an economic meltdown and is suffering from a shortage of foreign currency, despite the adoption of the US dollar and other currencies to stem galloping inflation which has hit 231 million percent.
Last year the country introduced bond notes, which are pegged to the US dollar, in an attempt to stem the crisis.
But the bond notes have not eased the country’s currency woes.
Mawarire’s subversion case will resume on Tuesday.