The objective of this paper was to compare the effectiveness of different materials for mouthguards in preventing oral and maxillofacial injuries during sports activities. The present study compares the stress-reduction and energy absorption capabilities of two other fused filament materials - poly(lactic-acid plus) (PLA+) and polycarbonate (PC), with Ethylene-vinyl acetate (EVA), which is the most commonly used material for mouthguard fabrication. Two human skulls were modelled, and a boxing glove simulated punches along the x, y, and z-axes with 5mm displacement with 1 kN force. Firstly, the maximum principal stress curve in the skull was compared for forces along the three perpendicular directions. Furthermore, the present study examines materials energy absorption properties, including their specific energy absorption characteristics and initial peak von Mises stresses. Additionally, a topology optimization approach is used to create an alternative design for a mouthguard to improve specific energy absorption. The model without a mouthguard showed the highest stress concentration of 32.298MPa in the teeth, followed by the EVA material, which resulted in a maximum principal stress of 28.525MPa. Fused filament 3D materials, such as PLA + and PC, on the other hand, showed better mechanical effectiveness in both lower jaw dislocation and lower maximum principal stress by 30.82% and 51.25% in the mandibular and maxillary teeth. Though EVA comparatively shows better specific energy absorption capability at 2.24kJ/kg post-optimization than PLA + and PC, the peak principal stress experienced in the mandibular region was comparatively higher. The topology optimization, however, improved the energy-absorbing capabilities of PLA + by 4.5 times, reaching 1.37kJ/kg and PC from 0.165kJ/kg to 0.38kJ/kg. This study demonstrates that PLA + and PC have better stress reduction capabilities than EVA and could be promising materials for the fabrication of mouthguards in sports activities. This study highlights the importance of topology optimization in dental materials science and engineering to develop safer and more effective mouthguard designs.