While making the announcement Paul Barber, the FA's director of marketing and communications, said "The Riverside is a terrific stage for international football and I'm sure we can look forward to a tremendous atmosphere in front of a capacity crowd in June".
The game could pitch several Boro players against each other. Szilard Nemeth is almost a certainty to start for Slovakia while Gareth Southgate, Ugo Ehiogu and Jonathan Greening will all be hoping for a place in the England squad.
Memories come flooding back from the match in Bratislava last year, when Nemeth gave Southgate a torrid time and pounced to give Slovakia a surprise lead.
England fought back to take the game 2-1 with goals from Michael Owen and David Beckham, but will be hoping for an easier ride this time.
Boro chief executive Keith Lamb said "As we have international players of both countries in our first-team squad, it is particularly appropriate that we should host a game between England and Slovakia. June 11 promises to be a proud day for Middlesbrough FC and its supporters."