Precisely considering the second order term in external tendon deformation, the natural frequency of externally prestressed beam is derived by energy method. It illustrates the effect of external tendon compression on beam natural frequency. The calculation results also show that the influence coefficient stating the softening effect of the external tendon compression mainly depends on the number of deviators. Without deviator, the eccentricity loss is maximum, the influence coefficient is 1, and the effect of external tendon compression is the same as that of the external axial force. As the number of deviators increases, the eccentricity loss decreases, the external tendon is close to the unbonded tendon, and the influence coefficient decreases to near zero, which is close to nought effect of unbonded tendon compression. For the beam with two or more deviators, due to the influence coefficient significantly less than 1, the external tendon compression softening effect is negligible. With the increase of the eccentricity and tendon area, the first natural frequency grows up, but the effect of the external tendon on other frequencies is negligible.