The case was been filed at the Zurich Commercial Court on Wednesday on behalf of a 17-year-old African player and his parents, who say that the rules make FIFA's transfer regulations unlawful.
A spokesman for Zurich law firm Nater Dallafior Rechtsanwaelte, which has brought the case, said in a statement that the player, who had represented his country at youth level, was unable to move to a club in the European Union because of the rules.
"Thereby, he and his family miss the probably unique chance of a professional and social advancement," said the statement issued on Thursday.
10 players to leave Man Utd as Ten Hag plans summer clearout – Paper Round
FIFA bans the international transfers of players under the age of 18 unless their parents have emigrated for reasons not connected to football or both the player and club are based within 50 kilometres of a national border.
The only other exception is for transfers within either the EU or European Economic Area (EEA), where the minimum age is 16.
In those cases, clubs must still ensure that the player continues his education and studies for an alternative career, as well as making sure he has a high living standard.
"FIFA implemented these regulations on the pretext that young football players such as the claimant must be protected," said the statement.
"In reality, however, these regulations lead to a discrimination of football players from third countries outside the European Union." This, it said, made them unlawful.
The statement said the rules also infringed EU law, which allowed for unrestricted free movement of students and employees.
FIFA could not immediately be reached for comment but has argued in the past that the rules go back to an agreement signed in 2001 between FIFA, UEFA and the European Commission and these had been further developed over the years.
Spanish clubs Real Madrid and Atletico Madrid have been banned from signing players for two transfer windows by FIFA for breaching the rules while Barcelona have completed a similar ban. All three clubs denied wrongdoing.
Former Cameroon international Jean-Claude Mbvoumin, who has set up the Culture Foot Solidaire group to fight the trafficking of minors, says that young African players are still brought to Europe by false agents.
He told Reuters last year that families sometimes hand over their life savings to the agents hoping to secure a move to a top club, only for their sons to be abandoned on the streets of Europe.
FIFA is also facing a legal complaint at the European Commission from the world players' union FIFPro, which says that the current transfer regulations have led to a lack of competition in the sport.
'It's his choice' - Deschamps on Giroud absence and Mbappe transfer news
Ancelotti 'calm' despite Champions League final and Mbappe rumours