Federation Internationale de Football Association says City broke rules on transfers for players aged under 18.
The Premier League club could have faced a transfer ban, but the disciplinary committee of world football's governing body instead imposed a fine of 370,000 Swiss Francs.
City's English rivals Chelsea are now serving a one-year transfer ban after also being found guilty by the body in February of breaching regulations relating to the recruitment of minors.
"The Club accepts responsibility for the breaches which arose as a result of misinterpretation of the regulations in question", City said in a statement.
City's offences relate to the transfers and registrations of players under the age of 18, which break FIFA's overall regulatory framework.
"The disciplinary committee took into account the fact that Manchester City accepted responsibility and sanctioned the club with a fine of 370,000 Swiss Francs".
"All of the breaches occurred before December 2016 when guidance on the interpretation of the provisions was issued, since which date Manchester City has been fully compliant".
Both clubs are in the European Union or European Economic Area and the player is aged between 16 and 18.
City are also facing a separate investigation from UEFA regarding financial fair play (FFP), which was opened in March. Chelsea launched another appeal in June to the Court of Arbitration for Sport.
In regards to global transfers of players aged under 18, they are only allowed in three circumstances: the players' parents have moved to the new country for non-footballing reasons, they and the club are based close to the relevant national border or the transfer takes place within the European Economic Area and the player is at least 16.