The charge relates to the purchase of Benjani from Auxerre in 2006 and then the sale of the Zimbabwe international last January. Both deals were done with agent Willie McKay representing the player and McKay has also been charged by the FA.
A spokesman for PFC has strongly denied that the club have broke the rules.
He said: "We did not pay an agent when Benjani joined the club from Auxerre in January 2006, and his transfer to Manchester City in January 2008 was approved at the time by the Premier League and the FA's compliance unit."
"This is nothing more than a technicality which we will strongly contest."
Both Pompey and McKay have until the 29th of August to respond to the charges.
This news isn't really what we wanted just before the season starts. Hopefully nothing comes of it and Pompey are found as innocent (I don't care what happens to money grabbing McKay).
This news is a reminder that the corruption in football investigation is still yet to be resolved and I hope and pray that there isn't an extremely nasty surprise at the end of it for us.