Bolton Wanderers legend Nat Lofthouse was absent from a plaque listing every England player's debut.
The FA was alerted by a Bolton fan shocked to see the "Lion of Vienna" missing from a pride of England stars.
Les Medley, who was a star of the "push and run" Tottenham team of the early 50s, was also missed out.
The FA has apologised to the families of both players.
"We appreciate this matter being brought to our attention and, following an investigation, have ascertained that it was due to a formatting error," said a spokesman.
"The panel is in the process of being taken down and will be replaced imminently"
The omission of England's sixth highest scorer, who netted 30 goals in 33 games, was spotted in the week when Wayne Rooney scored his 50th goal for England to break Sir Bobby Charlton's record.
Bolton's club historian Simon Marland said: "How can you miss a guy a who scored 30 goals in 33 games?"
"Anyone can make a mistake but on the positive side it's probably got people talking about Nat."
Lofthouse earned the nickname "The Lion of Vienna" because of his winning goal for England in 1952 against Austria following a run from the halfway line.
The Football Association has apologised for its own-goal in omitting one of England's most prolific scorers from a roll of honour at Wembley Stadium.