To improve the flexural behavior of thin bonded cement-based overlays, this study was carried out on the use of repair material incorporating amorphous metallic fibers (AMFs) in combination with the rubber aggregates obtained from grinding of worn-out tires. For this study, sixteen mortar mix compositions were prepared to contain AMFs and/or rubber aggregates to be used as overlay material while the substrate used was plain cement mortar. Rubber aggregates were incorporated at three different replacement ratios (i.e., 10%, 20% and 30%) by an equivalent volume of sand, and AMFs were added in three different dosages (i.e., 10 kg/m3, 20 kg/m3 and 30 kg/m3). In this study, composite beams (500 × 100 × 140 mm) comprising substrate (500 × 100 × 100 mm) and repair layer (500 × 100 × 40 mm) were prepared and investigated under flexural loading. Experimental results showed that the increase in rubber content resulted in a decrease compressive strength, flexural strength and modulus of elasticity. Rubberized fiber-reinforced cementitious composites (30R30F) exhibited higher flexural toughness and the flexural toughness improved up to 400%. Toughness and maximum deflection of composite beams enhanced significantly due to synergetic effect of AMF and rubber aggregates. It was observed that before peak load, rubber plays its role by delaying the micro-crack propagation. Results also revealed that the steel fibers reinforcement plays an important role in restraining the crack openings under flexure loading. In the post-peak region, steel fibers control the cracks from propagating further by bridging action and provide higher post-peak residual strength.