In conventional fuel systems, biodiesel is an effective and eco-friendly substitute for petro-diesel. However, their compatibility with nitrile butadiene rubber (NBR) remains a challenge. This study reports that specific doses of gamma radiation can improve the compatibility of NBR with biodiesel and petrodiesel blends. Using small-amplitude oscillatory shear (SAOS) rheology and positron annihilation lifetime spectroscopy (PALS), we correlated the changes in the volume and weight of NBR after immersion in fuel blends with microstructural characteristics. Our results show that gamma radiation can significantly improve the compatibility of NBR with biodiesel but not with petrodiesel. Higher radiation doses significantly constrained NBR chain relaxation dynamics, as indicated by the increased relaxation modulus. PALS measurements showed reduced freevolume hole radii with increased radiation dose. Furthermore, we observed that the fuel diffusion mechanism was diffusioncontrolled; however, the initial chain relaxation process played a role in the ingress of biodiesel into the NBR matrix. Our study highlights the potential of radiation processing to improve the biodiesel compatibility of NBR, which could lead to the development of efficient fuel-compatible NBR-based components.