Dozens of environmentalist activists greeted the 16-year-old in the early afternoon after waiting several hours for her to arrive at a marina in Portugal's capital.
She made the three-week journey on a catamaran with a British navigator and an Australian sailing couple after the summit was moved from Chile to Madrid because of unrest in its original host country.
The boat, La Vagabonde, carried the Swedish campaigner, who refuses to travel by plane, across the ocean so she could attend the COP25 climate summit in Madrid.
"I think people are underestimating the force of angry kids", she said.
She wanted a low-carbon form of transport to get to the climate meeting.
"Estimated time of arrival right now is Tuesday morning [local time]".
Thunberg started her journey on November 13 from the United States on a solar-powered catamaran to avoid contributing to carbon emissions. We'll be arriving at Doca de Alcantara, Lisbon.
"We are watching you".
Preliminary temperature measurements show that the years from 2015 to 2019 and from 2010 to 2019 "are, respectively, nearly certain to be the warmest five-year period and decade on record", the World Meteorological Organisation said. Her act of resistance soon became a global movement, with millions of youth around the world leaving school and taking to the streets to demand swift action to halt the climate crisis.
This year was hotter than average in most parts of the world, including the Arctic.
The conference kicked off on Monday with UN Secretary General Antonio Guterres warning that the planet had reached a "point of no return".
Delegates at the talks aim to finalise groundwork to support the Paris pact to curb the rise in global temperatures, which enters a crucial implementation phase in 2020.