The 24-year-old joined Royals on loan from parent club QPR in January and went on to make five appearances before suffering an ankle injury at Millwall.
He returned to play the final game of the season at Birmingham City, but now faces an uncertain summer after admitting he is not sure where he will be next season.
"Right now, I have no idea what the future holds. I still have one year left on my contract at QPR and I respect and honour that. I don't know how Mark Hughes [QPR manager] feels or has in his mind or what players he wants to keep, but I will go back there for pre-season and train," he said.
"Until I speak to them I don't know what's going to happen. Whatever happens over the summer happens, I'm not sure."
With QPR battling relegation from the top flight, Connolly is not even sure whether he will be playing Premier League football next season or not.
But asked whether he would like to stay at the Madejski, the defender said it 'felt like home' from the moment he joined.
"They are an amazing group of players and staff and it helped a lot. Brian [McDermott] is a great manager and I've had a great time here. But I have one more year with QPR," he commented.
"Every player wants to be wanted and I'm not sure what Brian is thinking at the moment but it's nice to have options."
While Connolly's future is unclear, Reading have confirmed that Andy Griffin, Brian Howard and Tomasz Cywka will not be staying with the club this summer.
Also shown the exit door are Cedric Baseya, Cameron Edwards, Ethan Gage, John Goddard, Simon Locke, Carl McHugh, Jack Mills, David Murphy, Frankie Raymond, Dan Carr, James Murphy and Jacob Walcott.
"On behalf of everyone I want to thank every single player for their contribution to the club," said director of football Nick Hammond.
"There are so many examples, right from Andy Griffin, who was Brian's first signing, up to Tomasz Cywka who made an impact this season both on the pitch and with his personality around the group, but it is not just those two, everyone goes with our very best wishes and gratitude."
Ian Harte is in talks over a new deal and 36-year-old Brynjar Gunnarsson is also in discussions about his role and the options open to him.
Benik Afobe has returned from his loan spell to Arsenal and Hayden Mullins' loan deal from relegated Portsmouth has also concluded.