Counter terrorism police raided several homes across the city on Thursday as part of an ongoing investigation.
Memhet Biber, 25, allegedly travelled to the Middle East in 2013 with the al-Nusra Front, a Syria-based jihadist group at that time linked to al-Qaeda.
A 17-year-old suspect is accused of attempting to travel in 2015 to fight with the Islamic State (IS) group.
The Australian government has made it a criminal offence under to take part in, fund, recruit or train for the conflict with IS, or to travel for certain areas in Syria and Iraq under IS control.
Police were quick to defend the amount of time between the alleged offences and the arrests, saying a lack of law enforcement in the region made it hard to gather evidence.
"We ensure that we continue to take the matters of foreign incursion very seriously," Assistant Commissioner Neil Gaughan told reporters.
Police also said that the involvement of a teenager was troubling.
"We have a juvenile who appears to be involved, and we will allege is involved potentially in wanting to engage in hostile activities, and this is a continuing concern for us," Deputy Commissioner Catherine Burn said.
Mr Biber was one a group of men that convicted terror recruiter Hamdi Alqudsi helped travel from Australia to Syria to fight alongside IS militant.
Alqudsi was the first person to be prosecuted under Australia's foreign incursion laws and was in August sentenced to six years in jail.
Photos posted to Mr Biber's Facebook page in 2013 show bombed buildings, injured children and a dead aid worker in Syria.
Prime Minister Malcolm Turnbull said such cases showed why the government "continues to give these agencies the resources and the legislative powers they need to keep us safe".
Two men have been arrested in Sydney on suspicion of breaking Australian laws on involvement in foreign conflicts.