The charge, which the club admitted, relates to agency activity carried out by Willie McKay for Wigan in relation to the signing of Marc-Antoine Fortune.
Wigan were also warned as to their future conduct.
Meanwhile Mr McKay, who also admitted breaching The FA's Football Agents Regulation C10(a)(i) in relation to the same player signing, has been warned as to his future conduct and had his Overseas Agent Registration suspended for nine months, subject to any appeal. The suspension is, however, stayed for a period of two years.
Mr McKay, as an Overseas Agent, will be reported to his licencing National Association (The Scottish FA) for this misconduct.