The 19-year-old made three Premier League appearances off the bench for the Clarets last season, including his senior debut against Liverpool in the second match of the campaign.
The Australian midfielder spent the second half of last season on loan at Oldham Athletic, where he played 15 times to help the Latics avoid relegation.
"I'm really excited to sign on loan for the season. I'm really excited to come here and work under Uwe Rosler and his staff. I want to hit the ground running and do my best to help the team," O'Neill told the club's official website.
Manager Rosler added: "Aiden is a player who we have had on our radar for quite some time. He is 19 years old, but he is far more matured than his age. He will add things to our team what we need, he is athletic, well skilled and we must give compliments to the coaching staff at Burnley for that.
"He is very ambitions, a good lad and I'm delighted to get him to us – I'm sure our department in central midfield will be strengthened. I'm really looking forward to working with Aiden."
O'Neill could make his debut for the club on Saturday when Fleetwood host Rotherham United in their first game of the new League One season.