The versatile teenager was signed in January from the Barca Residency Academy and headed to Patriots Point on loan.
He played 14 times for the Battery, scoring once, with all his league appearances coming off the bench. The 19-year-old scored his first professional goal in a 4-3 defeat by Indy Eleven earlier this month.
Hibs Academy chief Steve Kean said: “After his loan with Charleston Battery, EJ will come back to us an even better player and be able to hit the ground running this season.
“He’s a real athlete and has very high technical skills. His pace, power, and ability on the ball made him stand-out, and we want to take him to the next level.
“He will be a massive addition to our development squad and the games programme will allow him to progress further.
"This also shows how beneficial our partnership with Charleston Battery is as it provided EJ with an opportunity to play regularly and allowed us to get his work permit approved.
”We look forward to welcoming him to Edinburgh and being a big part of the club moving forward.”
Johnson featured as a trialist for a Hibs XI in a friendly win against Spartans in mid-October, and signed a long-term deal during the winter transfer window.
He can operate anywhere on the right and will feature for the revived development team which will be playing a series of games against teams from England in the 1875 Invitational, a friendly tournament involving Hibs, Blackburn Rovers, Brentford, Huddersfield, Middlesbrough, and Queens Park Rangers.
Hibs are likely to face under-23 teams, having already taken on youthful XIs from Brentford and Huddersfield over the past three years, and a series of friendly fixtures will take place at home and away throughout the 2022/23 season in a bid to add variety and challenges to the development squad’s footballing journey.
The Capital club have already made seven summer signings, with Rocky Bushiri and Ewan Henderson now on permanent deals after loan spells, while Nohan Kenneh, David Marshall, Lewis Miller, and Jair Tavares have all signed permanent deals and Momodou Bojang arrived on a season-long loan.