The environmental activist, 17, posted a photo of herself with a schoolbag on her back and her hands resting on bicycle handles on Instagram.
“My gap year from school is over, and it feels so great to finally be back in school again,” she added in a caption.
Swedish high schools are resuming classes this week but it is not clear which school Ms Thunberg is attending.
Ms Thunberg took a year off school in 2019 to raise awareness about climate change around the world.
She shot to fame in 2018 after her “school strike for climate”, which started as a solo protest but soon inspired many thousands of students across the world.
Pupils in the UK were among those who followed her lead, demonstrating outside the Houses of Parliament to show their concern about the climate emergency.
Ms Thunberg has been invited to speak at the UN, the European Parliament and the World Economic Forum at Davos.
She joined other young activists for climate talks with German chancellor Angela Merkel last week.
The coronavirus outbreak has prevented the Fridays for Future movement that Ms Thunberg inspired from holding its mass rallies in recent months, lowering its public profile.
Ms Thunberg was named Time magazine’s youngest Person of the Year, and was also nominated for the Nobel Peace Prize.
But she warned last week that two years have been lost in the fight against climate change because of inaction by political leaders.
In a joint editorial in the Guardian on August 19, Ms Thunberg wrote: “Looking back [over two years], a lot has happened. Many millions have taken to the streets… and on 28 November 2019, the European parliament declared a climate and environmental emergency.
“But over these last two years, the world has also emitted over 80bn tonnes of CO2. We have seen continuous natural disasters taking place across the globe. Many lives and livelihoods have been lost, and this is only the very beginning.
“[But] when it comes to action, we are still in a state of denial. The gap between what we need to do and what’s actually being done is widening by the minute. Effectively, we have lost another two crucial years to political inaction.”