O'Neill, speaking to BBC Newcastle, didn't attempt to hide his deep disappointment.
He said: "The news from the specialist is that Steven's ankle will have to be put in a non weight-bearing plaster for about a fortnight.
"After that it might be that he needs an operation, but one way or another he will miss the rest of the season and that is obviously a blow to us, following on from the news about Lee, who had an operation today.
"We've had to do without Lee for most of the season so that news was probably to be expected.
"I watched the Scotland game and saw Steven come down, and when the stretcher comes you do fear the worst. You hope the news might be a bit better, but it's not great and we have to get on with it.
"It's a blow for Fletcher and a blow for us. We could have done without it at this stage of the season."