Ashley Dyball, 23, had been travelling through Europe on a break from fighting with the YPG Kurdish militia in Syria.
On Facebook, where he uses the name Mitchell Scott, he said he could be deported to Australia to face charges.
It is a crime under Australian law to assist militant groups in the Middle East.
A spokeswoman for Australia's Department of Foreign Affairs said the agency was providing consular assistance to an Australian detained in Germany.
"Due to privacy constraints we will not comment further," the spokeswoman said.
Mr Dyball's lawyer, Jessie Smith, confirmed to the BBC on Thursday that he had been detained but gave no further details.
Mr Dyball said on Facebook he was being "charged as a terrorist" and would be sent to Australia.
According to Australian media, Mr Dyball's family want the Australian government to grant him amnesty from laws primarily designed to protect the country from militants returning home after fighting with IS.
Australia is on high alert for attacks by radicalised Muslims, including those returning home from fighting in the Middle East.
In June it was reported that another Australian man, Reece Harding, was killed fighting with the Kurdish YPG militia group against the so-called Islamic State in Syria.
An Australian man who has been fighting against the so-called Islamic State group (IS) says he has been detained in Germany on terror charges.