The company said the fine, which must be paid within 45 days, would only have a minimal impact on its annual profit.
Federal Court judge John Logan imposed the fine on Friday, following a ruling by the court in December that Flight Centre had engaged in anti-competitive behaviour.
In a case brought by the Australian Competition and Consumer Commission, Flight Centre was found to have induced Singapore Airlines, Malaysia Airlines and Emirates to stop offering international airfares that were lower than fares offered by the travel agency.
The court found Flight Centre had broken the law on five occasions between 2005 and 2009.
Flight Centre intends to appeal the December judgment, and on Friday said it may also appeal the penalties.
It says it has already changed the way it deals with airlines to comply with the Federal Court ruling.
“While we are comfortable that we comply with the law, we consider it appropriate to test the decision at an appeal,” managing director Graham Turner said in a statement.
“This will clarify our position and rights as an agent.”
Any appeals are likely to be heard in the 2014/15 financial year, Flight Centre said.
In the meantime, it will pay the $11 million, which it says will be mostly offset by an $8.7 million one-off gain made in its wholesale business during the first half of the 2013/14 financial year.
Flight Centre made a net profit of $111 million in the six months to December 31, and on Friday said it still expects to make an underlying annual pre-tax profit of between $370 million and $385 million.
That would be an increase of at least eight per cent from the previous year.
Flight Centre shares dropped 11 cents, or 0.2 per cent, to $52.02.
By Stephen Johnson and Drew Cratchley, AAP