The Department of National Parks, Wildlife and Plant Conservation will repatriate two orangutans to Indonesia under the Convention on International Trade in Endangered Species of Wild Fauna and Flora (Cites) treaty by the end of December.
The handover will be only the second time apes have been returned after 14 were sent back to Indonesia in 2015.
Thailand ratified Cites, an international treaty signed to protect endangered plants and animals, in 1983.
The first to be returned will be a nine-year-old female orangutan named "Kola", which was born in Thailand to parents originating in Indonesia. Kola's parents were sent back home in 2015.
The second ape is a seven-year-old male orangutan named "Giant", saved from a wildlife smuggler over five years ago. He has been in the care of the Ministry of Natural Resources and Environment ever since.
Both apes have been living in the ministry's wildlife breeding facility in Ratchaburi province.
A senior department official, who declined to be named, said another four orangutans will be returned to Indonesia.
Despite both the orangutans being born in Thailand, authorities found that the DNA of the pair matched perfectly with orangutans commonly found in Borneo and Sumatra in Indonesia.
Based on the Cites' regulation, confiscated wildlife must be returned to the country of origin.
The Thai government will cover all expenditure for shipping the apes back to Indonesia.
In March next year, Thai forestry officials will visit Indonesia to observe a project in which orangutans are released into the wild.