She arrived at 12.45pm local time to a welcome ceremony attended by Lisbon mayor Fernando Medina.
Thunberg, has become the face of young peoples' demands for climate action and made a point of making the journey back from September's New York climate summit by sea rather than fuel-guzzling plane.
She had expected to be heading for Chile, but the South American nation passed the hosting of the COP25 summit meeting to Spain after suffering a spate of deadly anti-government protests.
Thunberg, British navigator Nikki Henderson and the Australian family who own the vessel set sail back to Europe on the 14-metre (45-foot) La Vagabonde catamaran on November 13 from Hampton, Virginia, on a voyage of more than 5,500 kilometres.
The teenager has not yet decided when or how she will leave Portugal to get to Madrid, a spokesperson said, adding that one option could be an overnight train to the Spanish capital.
The climate summit, which opened Monday and runs to December 13th, brings together representatives of some 200 signatory nations to the 2015 Paris accord.
Thunberg rose to prominence after she started spending her Fridays outside Sweden's parliament in August 2018, holding a sign reading “school strike forclimate”.
Having used her appearance in New York to denounce governments for failing to act with sufficient urgency on the environment, Thunberg attended weekly green protests in several US cities before embarking on her long trip home. She is expected to join a climate march in Madrid on Friday.