The Spanish club has been sanctioned for breaking the rules in the case of 10 minors and been punished with a transfer embargo for two transfer windows and a fine of 450,000 Swiss francs.
The Spanish FA has also been fined for rule breaches in terms of registering the players and fined 500,000 Swiss francs.
FIFA said in a statement: "FC Barcelona has been found to be in breach of article 19 of the regulations in the case of 10 minor players and to have committed several other concurrent infringements in the context of other players.
"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 450,000 Swiss francs.
"Additionally, the club was granted a period of 90 days in which to regularise the situation of all minor players concerned."
The sanctions follow investigations conducted by FIFA's transfer matching system officials into under-18 players who were registered and participated in competitions with the club between 2009 and 2013.
FIFA's rules state international transfers of minors are only permitted under limited circumstances, and have to be ratified by FIFA's players' status committee.
The FIFA statement added: "The 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.
"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.
"Young football players are vulnerable to exploitation and abuse in a foreign country without the proper controls. This particular fact makes the protection of minors in football by the sport's governing bodies, especially by FIFA, even more important."
The Spanish FA, which violated article 19 of the regulations regarding the first registration of the players, has been given a period of one year in to "regularise their regulatory framework and existing system concerning the international transfer of minors in football".
Barcelona will almost certainly appeal against the transfer ban, which has cast a shadow of doubt over moves already agreed for Borussia Monchengladbach keeper Marc-Andre ter Stergen and Croatian 17-year-old Alen Halilovic, who turns 18 in June.
Barcelona have a trio of youth players from South Korea, including much-sought after 15-year-old striker Lee Seung Woo, plus other players from Africa.
FIFA only allows international youth transfers when one of three situations apply: the player's parents have moved country for their own, non-related reasons; the move takes place within the European Union if a player is aged between 16 and 18; or the player's home is less than 50 kilometres from the national border being crossed.
Ter Stergen told the Kolner Express newspaper in Germany that he was still planning to leave Gladbach in the summer, but that he was uncertain of Barcelona's situation.
"I have not heard anything about it and do not know what you want from me now," he said.
"I only know that at the end of this season I will leave Borussia Monchengladbach."