Polyether-ether-ketone (PEEK) is a recently commonly used high-performance thermoplastic material with high heat resistance, high chemical resistance, high water resistance, and high wear resistance. Polyether-ether-ketone products with complex structures manufactured through the 3D printing process of fused filament fabrication (FFF) are emerging in the medical field. However, similar to other plastics, PEEK materials are also hygroscopic. This may have an impact on 3D printed products. The effect of storage time of filament on 3D printed PEEK products under specific temperature and humidity conditions has not been further explored. This study is mainly to explore the moisture absorption of PEEK filament for different storage time and the effect of moisture absorption on the performance of 3D printed PEEK products. The correlation between storage time and moisture absorption is verified by experiment. It is found that moisture will affect the surface quality of PEEK products. In addition, the mechanical test results show that the increase in the amount of water absorbed leads to the decrease of material properties, such as tensile strength, density, and hardness. Therefore, it is recommended to store unused or leftover PEEK filaments under vacuum drying conditions. For PEEK filaments that are being printed, it should be ensured to replace them every less than 24 h.