The demonstrations outside the Sydney Opera House and in Melbourne's Federation Square opposed Hakeem al-Araibi's potential extradition to Bahrain.
"This is a young man who has been tortured by a country you are working with and are contemplating sending him back to," former Australian soccer team leader Craig Foster told the Sydney crowd in comments directed at Thailand.
The rallies focused on Thailand and Indonesia's proposed joint bid for Association of Southeast Asian Nations to host the World Cup in 2034.
"If you want to host the World Cup, you must allow the free transit of players and officials through your country," Foster said.
The Melbourne crowd chanted "save Hakeem" while Professional Footballers Australia chief executive John Didulica implored Thailand to remember Australia's help in rescuing 12 boys and their soccer coach from a flooded Thai cave in July.
The rallies also called for FIFA, soccer's governing body, to consider suspending Bahrain from future competitions.
"You cannot have the privileges of the international community if you are not prepared to live by its rules or behave by its standards," Didulica said.
The former Bahraini team player says he fled political repression in Bahrain. He had been sentenced there in absentia in 2014 to 10 years in prison for vandalizing a police station, which he denies.
Al-Araibi had been living in Melbourne and played for a semi-professional soccer team. The 25-year-old was detained upon his arrival in Bangkok in November and a court ruled in December he could be held for 60 days.
Thailand expects to decide within days whether to proceed with extradition to Bahrain.
Victorian Premier Daniel Andrews wrote a letter to the footballer to say "stay strong, mate. We will get you home."