FIFA have imposed a transfer ban on Barcelona for the next two transfer windows.
The Catalan club has been found guilty of breaching rules relating to "the international transfer of minors".
Barca, who can appeal the ruling, have also been fined £350,000 and told to regulate the situation within 90 days.
The investigation, conducted by FIFA's Transfer Matching System, took place during the course of the last year and focused on 10 minor players who were registered and participated in competitions with the club between 2009 and 2013.
The Spanish FA has been fined £339,000 for their involvement and must "regularise their regulatory framework and existing system concerning the international transfer of minors in football".
"The RFEF (Spanish Football Association) and FC Barcelona were found to have violated several provisions concerning the international transfer and first registration of non-Spanish minors with the club, as well as other relevant regulations with regard to the registration and participation of certain players in national competitions," read an official FIFA statement.
"The investigations concerned several minor players who were registered and participated in competitions with the club over various periods between 2009 and 2013.
"The (FIFA) Disciplinary Committee emphasised that the protection of minors in the context of international transfers is an important social and legal issue that concerns all stakeholders in football.
"Above all, the committee highlighted that while international transfers might, in specific cases, be favourable to a young player's sporting career, they are very likely to be contrary to the best interests of the player as a minor.
"On the basis of this analysis, the committee concluded that 'the interest in protecting the appropriate and healthy development of a minor as a whole must prevail over purely sporting interests.'"
Barcelona are yet to comment on whether they will appeal the sanctions.