In the United States, each year over 100 million tons of asphalt pavement material is reclaimed due to its multifold benefits. The use of reclaimed asphalt pavement (RAP) in preparing new asphalt concrete saves money, safeguards the environment, reduces waste in landfills, conserves other natural resources, and increases the durability and longevity of pavements. However, a high percentage of RAP in asphalt concrete can lead to developing premature failure of asphalt pavements due to fatigue cracking. On the other hand, the use of softening agents in asphalt binders can resolve these problems. To this end, two waste products, namely, waste cooking oil (WCO), and engine bottom oil (EBO) along with a commercial rejuvenator were evaluated in this study. The efficacy of these softening agents in aged asphalt binders has been investigated at micro- and macro-levels. Three types of Performance Grade (PG) binders, namely, PG 64-22, PG 70-22, and PG 76-22, each collected from two different sources, were blended with 25% RAP binders and different percentages (0%, 15%, and 20% by the weight of the binder blend) of the selected softening agents. Selected Superpave tests, the Atomic Force Microscopy (AFM)-based PeakForce Quantitative Nanomechanical Mapping (PFQNM™), and Fourier Transform Infrared Spectroscopy (FTIR) analyses were done on the unrejuvenated and rejuvenated binders. It was found that the rejuvenators improved the flow behavior of the RPA-modified binder samples. The AFM test results showed that the micro-level modulus and deformation values of rejuvenated binders were significantly less than those of their unrejuvenated counterparts. Similarly, distinct peaks were conformed in the FTIR peaks for EBO and WCO-modified binders. The EBO or WCO helped to reduce the RAP-blend binder’s viscosity (e.g., lower mixing and compaction temperatures) and increase its rate of relaxation rates (e.g., improved thermal cracking resistance). Experimental data suggest that 10% EBO or WCO has similar beneficial effects in terms of improving 25% RAP-blended binders’ fatigue and thermal cracking resistance compared to the commercial rejuvenator, whereas WCO was more effective in reducing stripping potential than EBO. The findings of this study will help pavement professionals in selecting suitable rejuvenators for the construction of pavements with high RAP contents.