We are investigating evaluation of radiation biological effectiveness in an accelerator driven boron neutron capture therapy with considering microscopic energy deposition. In this study, we estimated cell survival fraction in a simulated neutron field for Boron Neutron Capture Therapy (BNCT) in a case of operating Fixed Field Alternating Gradient (FFAG) accelerator at Kyushu University with using the Particle and Heavy Ion Transport code System (PHITS) coupled with Microdosimetric Kinetic (MK) model.