We derive an explicit form of the quadratic-in-fermions Dirac action on the M5 brane for an arbitrary on-shell background of 11D supergravity with non-vanishing fluxes and in presence of a chiral 2-form on M5. This action may be used to generalize the conditions for which the non-perturbative superpotential can be generated in M/string theory. We also derive the Dirac action with bulk fluxes on the M2 brane.