The effect of thermally induced stress on the fundamental and higher order modes of highly elliptical core optical fibers is studied in this work using a finite element method. The stress analysis is carried out and anisotropic refractive index change is calculated using the plain strain approximation. After considering the stress optical effect, the modal analysis of the fiber is performed to obtain the modal solutions. The modal effective index, modal birefringence, and field distributions of different modes of the fiber are presented. The modal birefringence of the fundamental and higher order modes as a function of ellipticity of such fibers are also presented. It is seen that change in ellipticity causes significant change in birefringence for fundamental and higher order mode of the fiber.