However, half of the fine has been suspended until the end of 2014 because the Bombers fully co-operated with the investigation, meaning the club will only pay $10,000.
The AFL launched an investigation last week when it became aware that up to a dozen unlisted players had trained at the club before last Wednesday's rookie draft without the club receiving official permission from the AFL.
AFL.com.au understands the club initially claimed to have lodged the paperwork late. However the details of when the actual transgressions took place are not known.
Several players who took part in training with Essendon were rookie-listed by other clubs at Wednesday's rookie draft.
AFL rules say that clubs are not permitted to request, invite, allow, require or direct a player who had attended a combine or state screening session to be tested, evaluated or to do any form of training with either the club or an associated club before being drafted.
An Essendon spokesman told AFL.com.au that the Bombers "accept the sanction imposed on the club by the AFL relating to this matter."
The sanction ends another dramatic week for the club in which the AFL asked the Bombers to clarify whether or not they were still paying suspended senior coach James Hird.
Hird was suspended for 12 months and the club was fined $2 million and excluded from the first two rounds of the draft in August for its governance of a supplements program during 2011-12.
