Clarence House tweeted images of Prince Charles shaking hands with the 17-year-old after his first keynote speech at the Davos World Economic Forum in 30 years.
The meeting came at the annual Swiss gathering of government and business chiefs which this year has been dominated by the growing threat of climate change.
Ms Thunberg told Prince Charles it was nice to meet him, adding that he must be "very used" to intense media attention.
— Clarence House (@ClarenceHouse)January 22, 2020
Charles replied that it had taken him years to get used to the limelight with Ms Thunberg saying she had not yet got to grips with it.
The Prince of Wales later told CNN: "She's remarkable. She represents one of the main reasons why I've been trying to make all this effort all these years because, as I said, I didn't want my grandchildren to accuse me of not doing something about this in time and of course there they are.
"All her generation, almost my grandchildren if you know what I mean, are all desperate because not nearly enough has happened - we've left it so late.
"I've always worried about the fact that so often in terms of humanity we leave everything too late.
"So you have to hit a brick wall and experience a catastrophe before anything happens but this time, with this kind of disaster we have engineered, it takes a huge amount to turn the whole thing back to how it should be, to restore the balance."
Earlier on Wednesday, Charles delivered his strongest warning on the environment yet as he told world leaders the next decade is crucial to saving the planet.
In his first keynote speech, Charles urged government and business chiefs to help the private sector lead "the world out of the approaching catastrophe".
The prince, who has long been known for his environmental campaigning, was pictured meeting and shaking hands with 17-year-old Greta following his passionate address.
He told leaders gathered at the Forum: "Ladies and gentleman, you all have a seat at the table as this must be the year that we put ourselves on the right track."
He added: "Do we want to go down in history as the people who did nothing to bring the world back from the brink, in trying to restore the balance, when we could have done? I don't want to.
"Just think for a moment, what good is all the extra wealth in the world gained from business as usual if you can do nothing with it except watch it burn in catastrophic conditions.
"This is why I need your help, your ingenuity and your practical skills to ensure that the private sector leads the world out of the approaching catastrophe into which we have engineered ourselves."
He added: "We simply cannot waste any more time. The only limit is our willingness to act. The time to act is now."
Charles travelled from St Gallen in Switzerland to Davos in a fully electric Jaguar I-Pace, rather than using a helicopter.
He warned the world is in the midst of a crisis that "is now I hope well understood".
He added: "Global warning, climate change and the devastating loss of biodiversity are the greatest threats humanity has ever faced."
He described his dedication to encouraging corporate, social and environmental responsibility as an "uphill struggle".
But he added: "Now it is time to take it to the next level. In order to secure our future and to prosper we need to evolve our economic model."
Yesterday, Swedish activist Greta Thunberg also warned that time was running out to prevent catastrophic warming, while President Trump used his speech to attack climate “prophets of doom” .