Tunneling rock wastes (TRWs), which are often open- or gap-graded in nature, have been increasingly recycled and reused for sustainable construction of unbound permeable aggregate base (UPAB) courses with high porosity and desired drainability. However, there is still a lack of sufficient understanding of long-term mechanical stability of such TRW materials subjected to repeated applications of moving wheel loads. This paper aimed to characterize and predict resilient modulus (Mr) behavior of the TRW materials used in unbound permeable aggregate base applications. To achieve this goal, five different UPAB gradations were designed based on the gravel-to-sand ratio (G/S) concept. In order to study their Mr behavior, the laboratory repeated load triaxial tests were conducted under different combinations of confining pressure and deviator stress as controlled by the levels of the shear stress ratio (SSR). The prediction accuracy of fourteen classical Mr prediction models was comparatively analyzed, from which the improved Mr prediction model incorporating gradation and stress variables was proposed for TRW-derived UPAB materials and further validated by external database accordingly. The results show that under the same G/S value and confining pressure level, the higher the SSR is, the greater the final Mr values are, and the more significant the effect of G/S on Mr is. Under the same SSR level, the increase of confining pressure alleviates the effect of G/S on Mr. There appears to exist an optimal G/S value of around 1.6–1.8 that yields the best Mr behavior of the TRW-derived UPAB materials studied. The improved Mr prediction model was verified extensively to be universally applicable. It can potentially contribute to balancing long-term mechanical stability and drainability of TRW-derived UPAB materials through gradation optimization. The findings could provide a theoretical basis and technical reference for cost-effective and sustainable applications of UPAB materials derived from TRWs.