A simple and scalable fabrication process of graphene nanoplatelets (GnPs)-reinforced polyether ether ketone (PEEK) filaments with enhanced mechanical and thermal performance was successfully demonstrated in this work. The developed PEEK-GnP nanocomposite filaments by a melt-extrusion process showed excellent improvement in storage modulus at 30 °C (61%), and significant enhancement in tensile strength (34%), Young's modulus (25%), and elongation at break (37%) when GnP content of 1.0 wt.% was used for the neat PEEK. Moreover, the GnPs addition to the PEEK enhanced the thermal stability of the polymer matrix. Improvement in mechanical and thermal properties was attributed to the improved dispersion of GnP inside PEEK, which could form a stronger/robust interface through hydrogen bonding and π-π* interactions. The obtained mechanical properties were also correlated to the mechanical reinforcement models of Guth and Halpin-Tsai. The GnP layers could form agglomerates as the GnP content increases (>1 wt.%), which would decline neat PEEK's crystallinity and serve as stress concentration sites inside the composite, leading to a deterioration of the mechanical performance. The results demonstrate that the developed PEEK-GnP nanocomposites can be used in highly demanding engineering sectors like 3D printing of aerospace and automotive parts and structural components of humanoid robots and biomedical devices.