The linear amplification of modal disturbances that lead to boundary-layer transition in two-dimensional/axisymmetric hypersonic configurations is strongly reduced by the presence of a blunt nose tip, and the mechanisms underlying the low Mack’s second-mode N-factor values at the observed onset of transition over the cone frustum are currently unknown. Linear nonmodal analysis has shown that both planar and oblique traveling disturbances that peak within the entropy-layer experience appreciable energy amplification for moderate to large nose-tip bluntness. The present study extends the previous linear analysis by including the nonlinear effects. Specifically, the harmonic Navier–Stokes equations (HNSE) are solved with a fully implicit formulation and the Newton–Raphson method. The increased number of degrees of freedom for the nonlinear system presents difficulties for solution strategies based on direct solution of the linearized system. Such difficulties are overcome by using the generalized minimal residual method (GMRES) iterative method with a preconditioner corresponding to a simplified Jacobian without the cross-derivative terms. The HNSE solver is verified by comparing with nonlinear parabolized stability equation results for the nonlinear evolution of planar waves in an incompressible Blasius boundary layer and in a Mach 6 flow over a blunt cone. Finally, nonlinear nonmodal results are presented for planar traveling disturbances over a blunt cone configuration with reduced transition N factor as measured in wind-tunnel experiments. The nonmodal analysis demonstrates that entropy-layer disturbances generated close to the nose tip can seed the amplification of higher-frequency Mack’s second-mode instabilities farther downstream and hence can lead to a reduction in the transition N factor.