We present a computational framework to obtain nonlinearly elastic constitutive relations of special Cosserat rods with surface energy. The framework allows the rod’s cross-section to have arbitrary shape and the rod material to obey arbitrary three-dimensional material model for its bulk volume and arbitrary surface energy model for its lateral surface. The kinematics of the Helical Cauchy–Born rule is used to first construct a family of six-parameter (corresponding to the six strain measures of rod theory) helical rod configurations in which the generated three-dimensional strain field is uniform in the rod’s arc-length coordinate. This uniformity allows the three-dimensional nonlinear equations of elasticity to reduce to just the rod’s cross-sectional plane wherein the cross-section’s boundary also experiences traction due to the inherent surface energy in the rod’s lateral surface. The solution of this cross-sectional problem yields the induced in-plane displacement and out-of-plane warping in the cross-section for arbitrarily prescribed strain measures of the rod. We then derive expressions for the induced internal contact force, moment and stiffnesses of the rod in terms of the solution of the deformed cross-section and the prescribed strains of the rod. A finite element formulation is presented to solve the nonlinear cross-sectional deformation problem and further obtain the induced internal contact force, moment and stiffnesses. The presented framework will be useful for modeling of nanorods where surface energy plays a dominant role. Several numerical examples are presented using the presented framework to illustrate the effect of surface energy parameters on the deformation of the nanorod’s cross-section and the nanorod’s bending, torsional, extensional and shearing stiffnesses. We also derive improved analytical formulas for the extensional and bending stiffnesses of isotropic rectangular nanorods in their reference state. These formulas reduce to the existing widely used formulas for a special choice of material parameters, i.e., when the surface Poisson’s ratio and the bulk Poisson’s ratio match thus highlighting the limitation of the existing formulas.