Barca's transfer dealings have come under huge scrutiny this season, with former president Sandro Rosell resigning after questions were raised over their close-season signing of Neymar.
The Brazilian official moved to Camp Nou for €57.1 million, though the striker's former club Santos only received a fraction of that and now the signing of youngsters from abroad in recent years has landed the Spanish champions in more hot water.
A FIFA statement read: "The FIFA Disciplinary Committee has sanctioned the Real Federacion Espanola de Futbol (RFEF) and Spanish club FC Barcelona for breaches relating to the international transfer and registration of players under the age of 18.
"The Disciplinary Committee regarded the infringements as serious and decided to sanction the club with a transfer ban at both national and international level for two complete and consecutive transfer periods, together with a fine of CHF 450,000 (€370,000).
"Additionally, the club was granted a period of 90 days in which to regularise the situation of all minor players concerned."
Halilovic joined on a five-year deal for an initial fee of €2.2 million, with the amount set to rise based on a number of clauses.
It is unclear whether the Halilovic deal formed part of FIFA’s investigation, but if the transfer embargo were to be upheld it would be a huge blow for the Catalan giants.
