The Swedish teen sailed to the Portuguese capital before heading to neighboring Spain to attend the U.N. Climate Change Conference taking place in Madrid.
Thunberg's appearances at past climate meetings have won her plaudits from some leaders - and criticism from others who've taken offense at the angry tone of her speeches.
Speaking shortly after disembarking, she told reporters and supporters that people are underestimating the force of angry kids.
Ms Thunberg was to be met in Lisbon by local dignitaries and other activists.
"It turns out I've travelled half around the world, the wrong way".More news: Appeals court rules against Trump on subpoenas for financial materials
The boat was provided by an Australian couple.
She wanted a low-carbon form of transport to get to the climate meeting.
Thunberg, her father, and the crew aboard La Vagabonde sailed for 20 days from NY on a yacht that saved on carbon emissions and reduced their carbon footprint.
After using her appearance in NY to denounce governments for failing to act with sufficient urgency on the environment, Ms Thunberg attended weekly green protests in several USA cities before embarking on her long trip back to Europe. We'll be arriving at Doca de Alcantara, Lisbon. "We are SO enormously blessed to have you as our climate change warrior angel - dedicating all your time right now and your life to fight so very hard!"
Climate activist Greta Thunberg says she feels "energized" after spending three weeks crossing the Atlantic in a catamaran.More news: Federal Bureau of Investigation offering up to $5M for information on whereabouts of alleged terrorist
Thunberg's arrival in Lisbon coincides with the release of a bleak report by the Geneva-based World Meteorological Organization.
This year was hotter than average in most parts of the world, including the Arctic.
The two-week gathering kicked off on Monday with UN Secretary General Antonio Guterres warning that the planet had reached a "point of no return".
Greta missed last Friday's climate strikes as heavy winds delayed her arrival to Lisbon, but she is due to join thousands of activists marching in Madrid this week on the fringes of the COP25.
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.More news: Huawei smartphones, networking equipment uses non-US components