In this paper, we investigated the influence of initial stress on the frequency equation of flexural waves in a transversely isotropic circular cylinder permeated by a magnetic field. The problem is represented by the equations of elasticity taking into account the effect of the magnetic field as given by Maxwell's equations in the quasi‐static approximation. The free stress conditions on the inner and outer surfaces of the hollow circular cylinder were used to form a frequency equation in terms of the wavelength, the cylinder radii, the initial stress and the material constants. The frequency equations have been derived in the form of a determinant involving Bessel functions and its roots given the values of the characteristic circular frequency parameters of the first three modes for various geometries. These roots, which correspond to various modes, have been verified numerically and represented graphically in different values for the initial stress. It is recognized that the flexural elastic waves in a solid body propagated under the influence of initial stress can be differentiated in a clear manner from those propagated in the absence of an initial stress. We also observed the initial stress has a great effect on the propagation of magnetoelastic flexural waves. Therefore this research is theoretically useful to convey information on electromagnetic properties of the material: for example through a precise measurement of the surface current induced by the presence of the magnetic field.