Ms Thunberg, Luisa Neubauer from Germany and Belgians Anuna de Wever van der Heyden and Adelaide Charlier were accompanied by a handful of climate protesters as they arrived at the chancellery for a 90-minute meeting.
They are the first high-profile talks the youth activists have held with a world leader since the start of the pandemic.
“We are here, we are loud, because our future’s being stolen,” the protesters chanted as Ms Thunberg was mobbed by photographers.
The 17-year-old shot to fame after starting her solo protests outside the Swedish parliament two years ago.
Students around the world began following her lead, staging regular large protests, and Ms Thunberg was invited to speak to political and business leaders at UN conferences and the annual World Economic Forum in Davos.
But the coronavirus outbreak has prevented the Fridays for Future movement that Ms Thunberg inspired from holding its mass rallies in recent months, dampening its public profile.
“I’m actually surprised that we were able to do this so quickly,” Ms Thunberg said after her meeting with Mrs Merkel.
“It feels good, I would say.”
The activists sought a meeting with Mrs Merkel because Germany currently holds the six-month rotating presidency of the European Union, which together with Britain accounts for 22% of all man-made greenhouse gas emissions.
Mrs Merkel has in the past lauded the youth activists for putting pressure on politicians to act against global warming.
Ms Thunberg said she appreciated being given the opportunity to talk to Mrs Merkel for 90 minutes, more time than the Chancellor spends with many world leaders.
“That really made it possible to have a more in-depth, deep conversation, which we really appreciated,” Ms Thunberg told the Associated Press.
Climate campaigners argue that governments around the world are doing too little to curb the emissions that are heating up the atmosphere.
In a letter sent to world leaders last month, Ms Thunberg and others called for numerous measures including ending financing for oil and gas projects and setting binding annual carbon budgets.
Ms Neubauer said Mrs Merkel appeared to take the science behind climate change seriously.
“She’s a physicist, so that’s a start,” Ms Neubauer said, adding that the Chancellor’s perspective was to focus on progress achieved during her 30-year political career – Mrs Merkel served as Germany’s environment minister in 1994-1998 – rather than the decades to come.
“We look (…) towards the future and we see how, well, bad it looks to us,” said Ms Neubauer.
“This discussion today was possibly at least the attempt to bring those perspectives a bit together.”
Ms Thunberg said the activists also discussed the EU’s emissions targets and the lack of willingness by governments to take decisive action soon.
“We are sort of in a loop where everyone blames each other because obviously no-one can do everything,” Ms Thunberg told the AP.
“So then no-one does anything.”
Mrs Merkel’s spokeswoman Ulrike Demmer said the German government recently agreed to to cut emissions by up to 55% over the coming decade compared with 1990 levels.
It also backs plans for an EU Green Deal and for making Europe the first “climate neutral” continent by 2050.
“The subject (of climate change) is an issue of central importance for the entire German government,” Ms Demmer said.
“As such, an exchange with (the activists) is certainly beneficial.”
Ms Charlier said Mrs Merkel had assured the group that she did not support an EU trade agreement with the Latin American Mercosur bloc that opponents say would be harmful to the environment and human rights.
Mrs Merkel’s office did not immediately respond to a request for confirmation.
The activists said they are hoping world leaders will start to treat climate change as a crisis, the way they are doing with the pandemic.
“Of course, we are in a health emergency globally and we are seeing second waves everywhere,” Ms Neubauer told the AP.
“Yet the climate crisis doesn’t pause.”
Ms Neubauer said activists are planning to stage another global “climate strike” on September 25, although the pandemic situation will determine whether it is held online or on the streets.
