O’Brien joined Bolton from Portsmouth in the summer of 2007.
The 29-year-old said: “I’m eternally grateful for the opportunity that Bolton gave me.
“The way the supporters, the manager Gary Megson and the players have treated me has made me enjoy my football as much as I ever have done.
“I’m delighted to stay and there’s plenty of hard work ahead of me now.”
He added: “From my point of view, I’m happy at Bolton so if they were happy to keep me then there was never a problem,” he added. “I’ll continue to work hard and hopefully we’ll pick up results.”