I am building a gable roof over a flat roof at our church.It is 9'wx9'l.How do I determine the height of the center rafter?

By center rafter do you mean ridge board or beam?

First determine how much overhang or eve you want to have.

Let's say that you want a 1' overhang. That would make your total width 11'.

Your run is then half that or 5" 6"

Next determine how much pitch you want. A 12 in 12 pitch (pitch that rises 12" for every 12" horizontal run) would mean that the top of your ridge board would be 5' 6". That's a pretty steep pitch (45 degrees). A 6 in 12 pitch (22.5 degrees) would make the ridge board half the run or 2"9" high.

Tell us the pitch you want.