Thunberg is being recognized "for inspiring and amplifying political demands for urgent climate action reflecting scientific facts," the prize foundation said.
It added that the 16-year-old, who has been nominated for the Nobel Peace Prize, "personifies the notion that everyone has the power to create change. Her example has inspired and empowered people from all walks of life to demand political action."
Created in 1980, the annual Right Livelihood Award honors efforts that the prize founder, Swedish-German philanthropist Jakob von Uexkull, felt were being ignored by the Nobel prizes.
The four winners will each receive 1 million kronor ($103,000).
The foundation also gave its 2019 award to Davi Kopenawa and the Hutukara Yanomami Association, representing Brazil's indigenous tribe, for protecting the Amazon forest and its people; Moroccan activist Aminatou Haidar "for her steadfast nonviolent action" for Western Sahara and Chinese lawyer Guo Jianmei for her work for women's rights in China.
Ole von Uexkull, the foundation's executive director and nephew of the founder, said "we honor four practical visionaries whose leadership has empowered millions of people to defend their inalienable rights and to strive for a liveable future for all on planet Earth."
An award ceremony is planned in Stockholm on Dec. 4, six days before the Nobel prizes are handed out.
Thunberg said in a statement by the Right Livelihood foundation that "whenever I receive an award, it is not me who is the winner. I am part of a global movement of school children, youth and adults of all ages who have decided to act in defense of our living planet."
It "is a huge recognition for Fridays For Future and the climate strike movement," she said in a statement.
Thunberg's campaign, begun on Aug. 20, 2018 when she held solitary demonstrations outside Sweden's parliament, skipping classes once a week to protest climate change. Her solo protest has inspired millions across the world to stage protests urging leaders to tackle global warming.
The Swedish award committee said Thunberg "tirelessly conveys her message: acknowledge the facts, realize the urgency of the climate crisis and act accordingly. She speaks at high-level conferences, meets world leaders, and gives guidance to a growing global movement."
Thunberg, who was called "a powerful voice of a young generation that will have to bear the consequences of today's political failure to stop climate change," is currently in New York where she attended a U.N. climate conference.
On Monday, Thunberg scolded the audience at the U.N. Climate Action Summit, repeatedly saying "How dare you." Thunberg said: "We are in the beginning of a mass extinction and yet all you can talk about is money. You are failing us."
Kopenawa and the Yanomami tribe were cited for "their courageous determination to protect the forests and biodiversity of the Amazon, and the lands and culture of its indigenous peoples."
Brazil has faced international anger for fires raging in the Amazon rainforest and led to criticism of far-right President Jair Bolsonaro's environmental policies.
Guo was given the award for "her pioneering and persistent work in securing women's rights," the award committee said, adding "she has helped thousands of disadvantaged women in getting access to justice."
Described as "an outstanding nonviolent activist and human rights defender," Haidar was cited "for her steadfast nonviolent action, despite imprisonment and torture, in pursuit of justice and self-determination for the people of Western Sahara."
The jury had considered 142 nominations from 59 countries.