Following a year-long legal wrangle, the FA has agreed to pay Interfocus what one source described as a "substantial six-figure sum".
An FA spokesman confirmed that a settlement had been agreed, but refused to give details. Interfocus chairman and chief executive Matthew Hooper declined to comment.
Interfocus pursued legal action over an alleged breach of confidence by the FA. It said it had presented the FA with ideas for using the Three Lions in marketing and educational materials, which the FA did not pursue.
Around a year later the FA unveiled the lion mascots before England's World Cup qualifying match against Finland.
The settlement follows an unresolved battle between ad agency Mother and ITV Digital's administrator Deloitte & Touche over ownership of brand icon Monkey.
Giles Crown, a communications lawyer at Lewis Silkin, said: "The intellectual property rights remain with the creator of the work. It is a generally misunderstood idea that if you pay for the creation of advertising and marketing materials, then you automatically own everything within it."