A thermodynamic analysis of the Be-Mo system has been carried out using the CALPHAD method. The formation energies of the four intermetallic phases of this system obtained from first-principles calculations were utilized to compensate for the lack of experimental information on the phase boundaries and thermodynamic properties of this binary system. The optimized thermodynamic parameters reproduced the characteristic features of the phase diagram quite well. Our first-principles calculations show that the stable BeMo₃ phase may not have the Cr₃Si-type cubic structure reported in a previous study, because of its lower stability. The first-principles calculations also imply that BeMo with a CrB-type orthorhombic structure may be the stable phase in the ground state.