The world's football governing body turned down the Catalan club's appeal to overturn a two-window transfer ban, which was handed to them in April due to concerns over the "international transfer of minors".
Barca recruited five players this summer, including Luis Suarez from Liverpool, while their suspension went on hold during the appeals process, however, and have vowed to continue the fight.
A club statement read: "Regarding the resolution handed today by FIFA's appeal committee with regards to the transfer and registrations of players under 18, FC Barcelona announces that it will continue to defend its interests to the highest sporting legal court, in this case the Court of Arbitration for Sport (CAS).
"FC Barcelona cannot agree in any way with the resolution that goes against the spirit of our Masia (Barcelona's youth academy), an example of academic, human and sporting development, recognised worldwide."
Barca were found guilty of breaching FIFA's rules on the transfer of players aged under 18.
The players in question were registered and participated in competitions with the Catalan club between 2009 and 2013, while the Spanish Football Federation (RFEF) was also sanctioned by FIFA for the same breaches.
As things stand, Barca - once this transfer window is closed - will not be able to make another signing until January 2016.
FIFA's statement on Wednesday morning read: "Barcelona is to serve a transfer ban which will see the club prevented from registering any players at both national and international level for two complete and consecutive transfer periods, starting with the next registration period (January 2015) given that the appeal of the club had been granted suspensive effect by the chairman of the FIFA appeal committee.
"FC Barcelona has also been ordered to pay a fine of CHF 450,000 (£295,000) and been given a period of 90 days from today in which to regularise the situation of all minor players concerned."
The RFEF also saw its appeal turned down on Wednesday and has been fined.
FIFA's statement added: "The RFEF has been ordered to pay a fine of CHF 500,000 (£330,000) and granted a period of one year in which to regularise their regulatory framework and existing system concerning the international transfer of minors in football."