McPake missed the William Hill Scottish Cup final defeat by Celtic through the injury in May and has been in and out of the squad this season.
Now he will seek a more permanent solution to the problem, although it is unclear how long he will be out for.
Manager Terry Butcher said: "James trained two weeks ago and his back flared up again. He was going to have an operation at the end of last season but it was felt perhaps rest over the summer would be good. It hasn't been the case.
"He has had quite a few injections this season and it has come back to the scenario where an operation is hopefully going to sort things out and he can get back to action next year. We are looking forward to that very much.
"He has been a very good captain for Hibernian Football Club. Now he is not the captain and Liam Craig is, he has helped Liam out enormously with tasks and what to do. He has been fantastic."
Meanwhile, midfielder Kevin Thomson is set to return to training on Thursday after missing the William Hill Scottish Cup win at Ross County with a hip flexor injury.
Scott Robertson is also expected to be fit for Butcher's home debut against Partick Thistle on Saturday after coming off with a tight hamstring in Dingwall.