The suit, filed in Fifa's home city of Zurich with the backing of the largest labour union in the Netherlands, calls on Fifa to force Qatar to adopt "minimum labour standards" for migrant workers preparing for the tournament, including at least the right to quit a job or leave the country.
The Gulf state has faced criticism of its treatment of foreign workers from Amnesty International, the Building and Wood Workers' International organisation and others.
Repon Chowdhury, secretary general of the Bangladesh Free Trade Union Congress, confirmed the organisation had joined forces with Dutch union FNV in the suit on behalf of a Bangladeshi man who says he was harshly exploited in Qatar.
It joined the suit as co-petitioner after failing to get compensation from the man's employer, Qatar or Fifa, he said.
"We tried to settle the issue amicably, but all our efforts failed and ultimately we had to file a petition," Chowdhury said.
"As the umbrella body of trade unions, we feel that his right as a human being has been denied and we strongly raised our voice against this violation of rights."
A Qatar government spokesman had no immediate comment. Doha has previously denied exploiting workers and says it is implementing labour reforms.
Under Qatar's "Kafala" system, foreign workers must get their employer's consent to change jobs or leave the country. Qatar will pass a law next week that lets workers appeal to the government if their employer stops them leaving the country.
Critics say workers will still find it hard to change jobs or travel.
Gas-rich Qatar is pursuing a $200bn infrastructure upgrade and has recruited hundreds of thousands of workers from countries such as India, Nepal and Bangladesh. Foreign workers outnumber the local workforce by nearly 10 to one and can be jailed or deported for forming unions or holding protests.
Fifa was not immediately available for comment. In the past, it has cited plans under discussion to set up a group to monitor working conditions in Qatar.