In this study, the possibility of using ionic liquids (ILs) as auxiliary substances improving the vulcanization and physicochemical properties of natural rubber (NR) biocomposites filled with nanosized silica was investigated. Hence, the influence of ILs with bromide and chloride anions and various cations, i.e., alkylimidazolium, alkylpyrrolidinium and alkylpiperidinium cation, on the curing characteristics and crosslink density of NR compounds was determined. Furthermore, the effect of nanosized silica and ILs on the functional properties of the obtained vulcanizates, including mechanical properties under static and dynamic conditions, hardness, thermal stability and resistance to thermo-oxidative aging, were explored. Applying nanosized silica improved the processing safety of NR compounds but significantly increased the optimal vulcanization time compared to the unfilled rubber. ILs significantly improved the cure characteristics of NR compounds by increasing the rate of vulcanization and the crosslink density of NR biocomposites. Consequently, the tensile strength and hardness of the vulcanizates significantly increased compared to that without ILs. Moreover, the use of nanosized silica and ILs had a favorable impact on the thermal stability of the vulcanizates and their resistance to prolonged thermo-oxidation.