Hakeem Alaraibi, a former player for Bahrain's national side, was stopped on an Interpol red notice after arriving in Thailand from Australia on November 27 for a vacation with his wife.
The 25-year-old was granted refugee status in Australia in 2017 and has spoken out about being arrested and beaten at the start of Arab Spring protests in the Gulf state in 2012.
He was convicted in absentia on charges of vandalising a police station but said he was out of the country playing in a match at the time of the alleged offence.
Thailand's immigration chief Surachate Hakparn told reporters Alaraibi had been remanded for 12 days starting December 3 to give authorities time to examine documents submitted by Bahrain.
The Australian ambassador told him Canberra wants to get the footballer back, Surachate said.
"If there is proof that the arrest warrant is invalid... then immigration will repatriate him to Australia," he added.
The Bahrain embassy in Bangkok did not immediately respond to a request for comment.
Alaraibi told AFP in an interview Tuesday he believes Bahrain is "very angry" with him for interviews he gave in 2016 with mainstream media outlets about his treatment in custody.
"I'm not feeling well because I don't know what's going on," he said, adding that he feared being killed if sent back to Bahrain.
The oil-rich Sunni-led country, home to the US Fifth Fleet, crushed Arab Spring protests by its Shiite majority.
Alaraibi believes he was targeted because he is Shiite and due to his brother's political activism.
He also opposed the FIFA presidential candidacy of Sheikh Salman bin Ebrahim al-Khalifa, a member of Bahrain's ruling monarchy and president of the Asian Football Confederation.
Alaraibi plays for semi-professional club Pascoe Vale FC in Melbourne and came to Thailand for a holiday before going back to train.
The football club has been tweeting out a GoFundMe drive in a bid to help raise money for legal fees.
Thailand does not recognise refugees and has faced international criticism for sending them back to countries where they could face persecution.
Brad Adams, Asia director at Human Rights Watch, said the Interpol red notice should have been lifted because of Alaraibi's status as a refugee.
"What we're seeing develop is a Thai-sponsored tug of war between Australia and Bahrain in which Bangkok is conveniently forgetting that Hakeem is a refugee recognised by Canberra," Adams said.
Thailand has no reason to return him to Bahrain "where he will face torture and imprisonment for daring to speak truth to power," he added.