Fused deposition modeling (FDM) of carbon fiber-reinforced polycarbonate (PC-CF) is increasingly used in medical applications due to its excellent strength-to-weight ratio and adaptability for custom geometries. However, sterilization is a critical step that may compromise the structural integrity of polymer composites. This study investigates the effects of two low-temperature sterilization methods—ethylene oxide (EO) and hydrogen peroxide vapor (HP)—on the mechanical, thermal, and viscoelastic properties of FDM-printed PC-CF parts. Characterization included tensile, impact, and hardness tests; thermomechanical analysis (TMA); and dynamic mechanical analysis (DMA). EO sterilization resulted in approximately 20% reduced elongation at break and lower glass transition temperature, indicating a loss of ductility and thermal stability. HP-treated samples showed reduced stiffness (16% in Young modulus) but increased Tg and reduced thermal expansion, suggesting improved dimensional stability. DMA results confirmed distinct viscoelastic behavior between treatment types. These findings provide evidence for selecting appropriate sterilization protocols for FDM-manufactured PC-CF components used in functional medical devices.