The 22-year-old signed a three-year deal with the Athens based side and will wear the number 47 jersey.
Akpom was loaned out by Arsenal in the winter transfer window to Belgian First Division side Sint-Truidense V.V. where he impressed on loan.
Several clubs were interested in the Nigerian forward but he opted a move to Greece.
The youngster has been shipped out on loans to League one and Championship sides such as Brentford, Coventry City, Nottingham Forest, Hull City and Brighton and Hove Albion.
Arsenal and PAOK both confirmed the agreement for his move through video clip posts on their official Twitter handle.
He joined the Arsenal academy at the age of six and went on to sign his first professional contract for the Gunners at the age of 17.
He thanked Arsenal for his development through a post on his official Instagram handle.
The message read, "Wow. Leaving @arsenal after 16 years. From playing in the streets of Newham, I never in my wildest dreams thought I would have the honour of playing for Arsenal.
"I want to say a massive thank you to everyone associated with this club, especially you amazing fans who have always supported me. Excited for this next chapter in my career. Let’s go!"
He was unable to get game time consistently with and made a total of 12 appearances for the first team.