The 2016–17 season started well with the signings of defender Rhys Williams from English club Middlesbrough and promising 19-year-old midfielder Brandon Wilson, as well as the resigning of reigning Johnny Warren Medalist Diego Castro. After an inconsistent season the club finished 5th, with Castro sharing the club Golden Boot with Andy Keogh and Adam Taggart. They again faced Melbourne City in the elimination final, with the club shock winners 2–0 away from home to set up a semi-final with the newly crowned A-League Premiers Sydney FC. Sydney took a 3–0 halftime lead which they never relinquished, the Glory falling one game short of their second A-League Grand Final.
