Two police officers lifted Thunberg and dragged her away before putting her down on the ground some 20 metres away from the door she had been obstructing.
Thunberg and dozens of other environmental campaigners started blocking the main entrances to Sweden's parliament on Monday in a sit-down protest against the effects of climate change and what they said was political inaction.
The activists left on Monday afternoon but returned to protest on Tuesday morning.
Thunberg, 21, became the face of young climate activists as her weekly protests, starting in 2018, in front of the Swedish parliament quickly grew into a global youth movement with large rallies across continents.
Last year Thunberg was detained by police or removed from protests in countries including Sweden, Norway and Germany.
A British court last month acquitted her of charges of a public order offence as a judge ruled that police had no power to arrest her and others at a protest in London last year.