The 18-year-old midfielder has played a big part in the Sports’ National League South season, being allowed to develop under manager Adam Murray.
His performances alerted a club over 300 miles away and Boro have paid an undisclosed fee to take him to the Riverside.
Johnson, who has featured 30 times this season for the south coast club, has been tipped for big things after securing an EFL move.
Chief Executive Alan Williams says he understands it’s hard to see young players go but feels Eastbourne couldn’t stand in his way.
He told the club’s website: “It’s never easy to make an announcement when you sell a player, it’s hard for the supporters to accept, especially when Brayden has been so good for us this season.
“But it’s also hard for the staff, football and non-football, who have all played their part in creating an environment where he has been able to thrive and shine.
“Special mentions obviously to Adam and his team for the exceptional coaching and development, to Nick the Chef for making sure he was well fuelled and to John and Kim – who’s pastoral care adds so much value to what we are doing.
“Please remember we have never gone back on what we said at the start of this journey – we are here to develop people into the best version of themselves.
“It’s neither correct or acceptable to do anything other than allow him to go, with our blessing and best wishes.
“Both myself, Simon and Adam have great pride in what has been achieved with Brayden and so should anyone who had the pleasure of watching him play.”
PHOTO EASTBOURNE BOROUGH FC