First, how big is the betta's tank and how often do you change the water? Have you measured the ammonia and nitrates?
Are you sure it is fungus (actually caused by a bacterial infection) and not ich? Bacterial body fungus looks like patchy cottony growths while ich looks like grains of salt. Is the fish eating and swimming about, or does he look and act really sick?
BettaFIX is great for preventing secondary infections caused by minor bumps and scrapes.
For a full blown infection, I would recommend BettaMAX, a true antibiotic. If you have a heater in the tank, you should turn it down a few degrees to slow bacterial growth.