Barkley, currently sidelined by a grade three hamstring tear likely to keep him out until November at the earliest, pulled out of the move at the last minute on deadline day despite travelling to London.
Barkley is in the final year of his contract, having rejected the offer of a new deal from Everton, but Koeman refused to say his Toffees career was over.
Koeman: “Of course it was a strange last day of the transfer window but I don’t think it was only that for Everton but for most of the Premier League clubs.
“Ross also came to see me last Tuesday and he explained to me why he turned down the chance to go to Chelsea. That is private.
“He was open to making a move to another club and I heard from the board that there was an agreement between Chelsea and Everton.
“But finally the decision was by the player. And that was what happened at that time.
When asked if Barkley’s Everton career was over, Koeman added: “No, because he is still an Everton player.
“To the end of this season he has his contract.
“Of course, the player at this time is injured and it will take another two or two-and-a-half months before he is available.
“So I don’t need to take that decision now and I can wait and see what will happen. Then we will see what the decision will be at that time.”