The 17-year-old youth was intercepted by counter-terrorism officers at Sydney Airport a fortnight ago, a media report said.
According to Immigration Minister Peter Dutton, the incident happened on March 12 at the international terminal.
"There was a male who was taken off a plane after being interviewed by counter terrorism unit (CTU) officers at the Sydney Airport," Dutton said.
"He was on his way to conflict in the Middle East and it comes off the back of two boys aged 16 and 17, who had been intercepted by Counter Terrorist Unit officers just before that," he said.
"Many of these young people, even without the knowledge of their parents, are downloading and receiving information through social media and on the Internet," Dutton said.
"This death cult (IS) is reaching through the computer screens into the minds of young Australians, brainwashing them and that is a great difficulty that all western democracies have."
Meanwhile, Prime Minister Tony Abbott said his government was making every possible effort to prevent youths from joining IS in in Iraq and Syria.
"My message to them is 'don't go, don't go'. It is very dangerous for you. It is very dangerous for others and we will do everything we can to stop you if you do try to go," Abbott said.
The duo was later released into the custody of their parents.
This month also saw Melbourne teenager Jake Bilardi travel to Iraq where he carried out a suicide bombing for IS.
The attack allegedly targeted an Iraqi armed unit west of Baghdad.
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