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Jackson, a Charlton legend who played 279 games for the club as a player, has guided the Addicks to seven wins in 10 games in League One as caretaker boss.
Charlton have said the 39-year-old has signed contract that will “automatically renew at the end of each of the next two seasons based on success on the pitch”.
Jackson said: “I’m very pleased and very proud. I have a special relationship with this football club, it is coming on 12 years now. I’ve been through some emotional times, highs and lows, which mould you into a certain character and this is the culmination of the story.
“From the moment I came here I had a special relationship with the supporters and the club and that has only grown over the years, through the good times and through the bad.
“The players have been absolutely brilliant. I can’t speak highly enough of them. The players and the staff have brought into what I am trying to do and they have helped facilitate results. I believe in everyone around me, I know that they are first class and will take the club forward.”
Charlton owner Thomas Sandgaard said: ““We have all seen the impact Johnnie has had since he took over. You can see that in the results, which have been excellent, and in the performance – the team are pressing with intensity, defending bravely and moving the ball quickly in possession. He’s doing an amazing job.
“Johnnie has a passion for the club, a connection with supporters, players and staff and a real knowledge of the game, so I’m delighted that he’s our new permanent manager.”