Federation president David Gallop announced the initiative at a ceremony at Parliament House in Canberra.
Dubbed "Football Cares," Mr Gallop says it was inspired by a similar move by the Italian club AS Roma.
He says the measure is aimed at aiding humanitarian efforts in Europe through the United Nations refugee agency and Football United.
Football United is a local not-for-profit organisation that uses the sport to promote social causes.
Mr Gallop says the public will be asked to donate to the international or domestic part of the campaign.
And he says the domestic element will involve providing assistance to the 12,000 Syrian refugees Australia will take in from the start of next year.
"We will be working with Football United to make sure that there are football drop-in centres, that there are coaching clinics, and that football gets behind these people as they come into Australia. It's a fantastic effort. It's just one of the ways that football shows what it can do in the community."
Mr Gallop says football is a universal sport.
And he says no sport reflects Australia's multiculturalism like football.
"When we recently played Bangladesh in Perth, our team had up to 15 cultural backgrounds just in the Socceroos. It's a sign of that extraordinary diversity that football embraces."
The son of Greek migrants, Socceroos coach Ange Postecoglou says football has played a significant role in his life.
"My parents made the pretty gutsy decision -- like a lot of migrant parents -- to come halfway around the world to a country where they didn't speak the language, they didn't know anyone. And I guess, initially, like all people trying to assimilate in a new country, it was pretty tough for them. But there were two places of worship on a Sunday that the local Greek community used to congregate, where my parents and my family felt comfortable. They both happened on a Sunday. Sunday morning was church. Sunday afternoon was the football pitch. My dad wasn't overly religious, so, thankfully, for me, he made the football pitch our sort of avenue to assimilate into this country. And for me, it played a massive role. I've said that my love of football comes from the fact that it gave me a link to my father."
Afghan refugee and Football United ambassador Shegofa Hassani offered similar sentiments.
"Like all refugees, there are many barriers you face coming to a new country. You have challenges such as language barriers, cultural barriers, but the one that most face is isolation. And what I discovered was, through football, I was able to overcome that barrier. But, initially, my family wasn't too fond of a female, a Muslim girl, playing football, so I faced that challenge. And through Football United, I convinced my parents to let me play football. And over the years, I've come a long way. I started off as a participant. Eventually, I became a youth leader and a coach. And in 2013, I had the amazing opportunity to represent Australia in the Pacific Youth and Sports Conference, as well as the 2014 Football for Hope teams. I was captaining that team."
Meanwhile, the Socceroos' World Cup hopes could go a long way to being decided in the next week.
The Asian champions go into crucial qualifying games this next week, starting with facing Kyrgyzstan on Thursday.
Australia currently sits second in Group B, with Jordan top of the group.
That follows last month's 2-0 loss to Jordan in the qualifying campaign.
Socceroos veteran Tim Cahill has dismissed the defeat as a minor setback and says he believes his side can bounce back.
"(We) pretty much got a wake-up call against Jordan the last game, and we're definitely going to go out all-firing, because we definitely need the three points." ot
The Socceroos will be without defender Matthew Spiranovic, due to a calf injury.
After Kyrgyzstan, they will then play Bangladesh in the next leg of the qualifiers in Dhaka next Tuesday.
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