The midfielder was forced off during the defeat to West Brom in November, before managing just six minutes of the 0-0 with QPR three days later.
The 24-year-old is suffering from medial ligament damage to his knee and O'Neill has confirmed that a prolonged spell out of action is in order - something the manger had suspected anyway.
"He'll probably be about another two months," the northern Irishman told reporters. "I knew the news wouldn't be too good. It could have been worse but obviously it could have been better."
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"I’ll make a late decision on Fletcher," the 60-year-old added. "He’s been down to see the specialist, who was relatively pleased with him.
“He’s had an injection and we will now have to see how that works. Steven didn’t train yesterday but hopefully he will today and we’ll see how he gets on.
“But the two games in four days is something we might have to consider.”