The 10-time European champion and city rival Atletico Madrid, who won the Spanish league title in 2014, have both been hit with transfer bans by FIFA for breaching rules relating to the registration of minors.
Real have been fined $360,000, while Atletico has been told to pay $900,000, and neither club will be able to sign players during the July 2016 and January 2017 transfer windows.
Top clubs often bring in young players and then develop them at their youth academies in the hope that they will go on to become major stars.
Competition is intense to attract the very best young players and in recent years FIFA has shown a willingness to monitor this market.
"FIFA works hard to protect the rights of players under the age of 18 -- whether male or female, amateur or professional," said a FIFA statement.
"This is done through the enforcement of regulations prohibiting the international transfer of minors, or the first registration of minors in a country other than their own, except in specific circumstances."
Both clubs were not immediately available for comment when contacted by CNN.
"The two clubs were found to have violated several provisions concerning the international transfer and first registration of minor players as well as other relevant provisions with regard to the registration and participation of certain players in competitions," FIFA added.
"Absolutely untrue," it said in response to the charges. "All players that play or have played in the junior teams of our club are or have been registered before taking to the pitch, as the RFEF (Spanish Football Federation) has certified to FIFA in writing from April 17 2015, as the record shows.
"Consequently, Real Madrid will appeal this decision by FIFA to all sporting bodies, considering it absolutely unacceptable."
Both Real and Atletico will be able to appeal their bans and in the meantime are allowed to sign players during the January transfer window, one of two opportunities during the year when clubs are allowed to sign players.
"The transfer ban, which does not affect the current registration [transfer] period at all, given that it opened before the decisions were notified, applies to each club as a whole -- with the exception of the women's, futsal and beach soccer teams -- and does not prevent the release of players," said FIFA.
It's the second time this season Real Madrid has been left red-faced due to an administrative error, after they were expelled from the Copa del Rey -- Spain's primary cup competition -- for fielding an ineligible player, Denis Cheryshev.
Atletico appear better prepared to cope with the transfer ban, having recently signed the youthful quartet of Angel Correa, Luciano Vietto, Yannick Ferreira Carrasco and Matias Kranevitter.
Both clubs have been given 90 days to regularize the signings of all minor players concerned.
Barcelona was given a similar ban in 2014, although the club managed to stall the suspension with an appeal and was able to sign Luis Suarez from Liverpool in the July 2014 transfer window.
The Catalan club was also able to buy players during its ban but not register them to play -- most notably Aleix Vidal and Arda Turan who made their debuts for the club this month once the suspension had ended.
Reports in Spanish media suggest Luca Zidane, son of newly-appointment Real Madrid boss Zinedine Zidane, is one of the players involved.