The Nigerian youth international centre back announced the move on Twitter, although Arsenal are still to confirm the move has been completed.
The 19-year-old tweeted: ‘Thank you everyone for the messages wishing me well on my move to Arsenal I’ve been overwhelmed by the amount and I’m truly grateful.
‘It was sad to end my ten year spell with charlton this summer but I can’t speak highly enough of all of the wonderful people I met during my ten years there & I wish all those at @CAFCofficial the best for the future as I will always have a soft spot for the club & it’s fans.
‘Delighted to announce that I have officially signed for @Arsenal FC. Can’t wait to see what the next two seasons here have in store for me.’
Ajayi has no first team experience with the Addicks, and spent the majority of last season on loan at Conference outfit Dartford.
Norwich City were thought to be the other Premier League club chasing his signature, and for a while seemed the favourites as Ajayi lined up for the Canaries in a pre-season fixture.
It now seems Arsene Wenger has won the race for the defender who has played three times for the Nigeria Under-20 side.