Chelsea have been handed a two-window transfer ban for breaching FIFA regulations over the registration of minors.
The Blues were also fined 600,000 Swiss francs (over £460,000) by FIFA's disciplinary committee for breaching article 19 relating to the transfer of 29 players aged under-18.
The Football Association has been fined 510,000 Swiss francs (over £390,000) for breaching the rules in connection with minors.
Chelsea "categorically refutes the findings" and will appeal.
Chelsea also twice breached regulations relating to third-party influence, article 18bis, FIFA said.
"The FIFA disciplinary committee has sanctioned the English club Chelsea FC and the Football Association for breaches relating to the international transfer and registration of players under the age of 18," FIFA's statement read.
"Chelsea was found to have breached art. 19 of the Regulations in the case of twenty-nine (29) minor players and to have committed several other infringements relating to registration requirements for players.
"The club also breached art. 18bis of the Regulations in connection with two agreements it concluded concerning minors and which allowed it to influence other clubs in transfer-related matters.
"The disciplinary committee sanctioned Chelsea with a ban on registering new players at both national and international level for the next two (2) complete and consecutive registration periods.
"This ban applies to the club as a whole – with the exception of the women's and futsal teams – and does not prevent the release of players."
The Press Association in January 2016 highlighted possible irregularities in the signing of Bertrand Traore by Chelsea.
Chelsea officially signed Traore in January 2014 – the first transfer window after his 18th birthday – but it emerged he played for the club more than two years earlier when he was 16.
FIFA on Friday would not confirm if Traore's transfer was one of the 29 for which Chelsea have been punished but it was the trigger for the investigation.
FIFA regulations prohibit the international transfer of players under 18, unless in specific circumstances not related to football. Players aged 16 to 18 can move within the European Union.
Prior instances of similar infractions involving other clubs have seen the clubs involved appeal their penalty, delaying the implementation of a registration ban and allowing them to sign players.
Chelsea announced their intention to appeal, saying in a statement: "Chelsea FC categorically refutes the findings of the FIFA disciplinary committee and will therefore be appealing the decision," the club statement read.
"The club wishes to emphasise that it respects the important work undertaken by FIFA in relation to the protection of minors and has fully cooperated with FIFA throughout its investigation.
"Initially, Chelsea FC was charged under Articles 19.1 and 19.3 in relation to 92 players.
"We welcome the fact that FIFA has accepted that there was no breach in relation to 63 of these players, but the club is extremely disappointed that FIFA has not accepted the club's submissions in relation to the remaining 29 players.
"Chelsea FC acted in accordance with the relevant regulations and will shortly be submitting its appeal to FIFA."
The FA indicated it would appeal against the decision.
A tweet from the @FAspokesperson account read: "The FA notes the decision of the FIFA Disciplinary Committee published today.
"The FA has co-operated fully with FIFA's investigations, although we have raised some concerns with FIFA regarding its disciplinary processes.
"The FA intends to appeal the decision. We will however continue to work with FIFA and Chelsea in a constructive manner to address the issues which are raised by this case.
"As this is an ongoing legal process it would not be appropriate to comment further at this time."
