The 21-year old broke down at training yesterday and now in danger of missing up to six weeks.
It is a major blow for the Jets but coach Branko Culina said Rooneyâ€™s fitness issues were a main reason he brought in strike reinforcements this year.
''There is not much you can do about it,'' Culina said. ''I know Sean's situation. In the 12 months I have been here he has never been fit for one reason or another. That is why we have improved our depth.
''Sash (Petrovski) and Labi (Haliti) are options but it is not just those two. It might also make us rethink how we want to play.''
In better injury news for the Jets, physio Paul Hazell said defender Nikolai Topor-Stanley may get some good news in the coming days after hobbling off the pitch against Adelaide United on Friday night with a quadriceps injury.
''If the MRI shows something he might miss a game, if it is clear we can declare him fit for Friday,'' Hazell said.