The 26-year-old Durham paceman fractured a bone in his ankle during a County Championship match against Surrey last month.
Wood had already been forced out of the current Bangladesh tour.
He is set to miss the five Tests against India, the first of which begins on 9 November, and the one-day series that follows in the new year.
England's national physiotherapy lead Ben Langley said the new injury is unrelated to the problems that required two operations last winter.
"It was only when we got him in for a second scan that we discovered he'd been playing on despite having fractured a bone," he said.
"There's no reason to think that when he's had this bone fragment removed, he won't be able to get back to bowling as well he has for Durham, England Lions and England in the second half of the 2016 summer."
England bowler Mark Wood is to have a third ankle operation and is likely to miss the Test series in India.