The Spaniard reckons the Brazilian became the 'leader' of the camp following his blockbuster move - something which he believe occurred because Lionel Messi was the in charge at Barça.
Speaking to French Football News, Emery admitted: "I know when I’m the main person responsible, and when I’m not.
"It’s a process that a coach has to live with and internalise, and that he assimilates with time and experience. In every club, you have to know what your role is and what role you have vis-a-vis the rest of the group.
"I am of the opinion that PSG’s leader is Neymar. Or that he is currently becoming it. Neymar came to PSG to be the leader, to go through this process to someday become the best in the world. At Manchester City, Pep is in charge. At PSG, Neymar has to be."
Things never ran smoothly between the pair last season, with Emery supposedly struggling to deal with the player's overbearing ego and sense of self entitlement.
Before working with Neymar, Emery had never before worked with a player of his profile and is said to have been dismayed by his star man's behaviour.
He added: "A few months ago, a PSG player said to me, 'Mister, this year you have changed.'It was obvious. I couldn’t be the same coach with and without Neymar. We went through a period of adaptation with the player."
Now manager of Arsenal, Emery will be hoping for a smooth transition with all his new players respecting him as the main man.