This study investigates the high-velocity impact response of fused deposition modeling (FDM)–fabricated Kevlar–Onyx composites with different fiber stacking architectures, combining ballistic experiments and finite element simulations. Four configurations—unidirectional (UD), quasi-isotropic (QUA), helicoidal (HEL), and cross-helicoidal (CHL)—were manufactured using a Markforged Mark Two system and subjected to ballistic impact tests with steel projectiles at velocities up to 600 m/s. Post-impact damage was characterized using high-speed imaging and X-ray computed tomography to quantify penetration depth, rear-surface bulging, and internal failure mechanisms. Finite element models were developed in LS-DYNA by explicitly discretizing individual Kevlar filaments within each printed layer, informed by experimentally observed damage patterns. Experimental results showed that the UD configuration exhibited the poorest impact resistance, whereas QUA, HEL, and CHL configurations provided moderate improvements. However, contrary to expectations based on bio-inspired designs, helicoidal architectures did not demonstrate a substantial enhancement in ballistic performance under high-velocity loading. Both experiments and simulations revealed that failure was dominated by inter-filament separation within layers rather than fiber fracture or classical interlaminar delamination. These findings indicate that, for FDM-fabricated composites, filament-level bonding and interface integrity govern high-velocity impact behavior more strongly than macroscopic stacking sequence. The presented modeling framework highlights the necessity of filament-resolved simulations to accurately predict dynamic failure in additively manufactured composite structures.