Isaac Byungdo Lee was arrested Monday in Nong Khai province, along the Thailand-Laos border, 620 kilometres northeast of Bangkok.
A pick-up truck belonging to Lee was found in the vicinity of several North Koreans who were believed to have entered the country illegally, said Pol Col Panlop Suriyakul na Ayutthaya, chiefof the Nong Khai Immigration Bureau.
Lee, a Christian missionary, allegedly has a history of helping North Korean refugees enter the country before directing them to the South Korean embassy or facilitating their journey to the United States through Christian networks.
Lee was being held in the city of Sri Chiang Mai while awaiting trialon charges of human trafficking, Panlop said.