The paper discusses dynamics of charged particles and neutrons in boron neutron capture therapy system (BNCT) as well as geometrical and physical optimization of BNCT system elements. Our choice is BNCT system with linear accelerator. BNCT track includes ion injector, RFQ, DTL, neutron-producing target and neutron moderator which provides an exit (last collima-tor) flux of epithermal neutrons satisfied to International Atomic Energy Agency (IAEA) requirements. The fol-lowing software tools IBSimu, LIDOS, COMSOL Mul-tiphysics and PHITS were used for modelling BNCT system.