"The North Koreans have been transferred to the immigration detention centre to be processed to go to South Korea if it is their wish," UNHCR spokeswomen Kitty McKinsey told Agence France Presse.
The defectors, mostly women and children, were discovered Tuesday after they made the long trek across China and through Laos to enter Thailand.
"They will be deported to a third country because normally North Korean defectors don't want to go back to their home country," said Suwat Thamrongsrisukul, Bangkok's immigration police chief.
He did not give a date for the deportation of the 59 North Koreans.
Police Major General Praphan Panikom said Wednesday that the migrants had been charged with illegal entry and sentenced to six months in prison, but said the court had ordered them to be handed over to immigration police instead.
Previous groups of North Korean defectors have received similar sentences, but they usually end up being accepted by South Korea rather than being sent home.