The second-year key forward fell awkwardly on the arm and will have scans on Thursday to determine if surgery is required.
Fremantle has already lost Anthony Morabito for the entire 2011 season with a serious knee injury, while veteran defender Roger Hayden (foot) is not expected to play until mid-year.
Houghton, while expected to miss up to eight weeks, will still be able to run and build his fitness base.
The 19-year-old was recruited with pick No.36 at the 2009 NAB AFL Draft and played nine senior WAFL games with Perth in his first season.
