In this paper, a new semi-analytical solution is proposed to describe the interactions between ocean waves and a flexible cylindrical net cage that is submerged at different depths below the mean water level. The flexible net is treated as a thin perforated shell, and its deformation is governed by the membrane vibration equation of cylindrical shells. The small-amplitude wave theory is adopted to simulate the wavefield, while the flow passing through the cage is described by the porous medium theory. The numerical results exhibit significant wave responses of the net cage, including the distribution properties of wave surfaces, dynamic pressure drops on the net interface, and net structure displacements. Furthermore, the influences of several important design parameters on the hydrodynamic action imposed on the net cage are revealed by parametric studies. The present studies conclude that the significant wave impact is mainly concentrated on the free water surface, and increasing the porosity and flexibility of the net can alleviate wave scattering and the hydrodynamic actions. In addition, at specific wave frequencies, the horizontal wave force acting on the cage will vanish. These findings should be useful to engineers who are designing offshore fish cage systems.