Background: Among additive manufacturing techniques, the filament-based technique involves what is referred to as fused deposition modeling (FDM). FDM materials are currently limited to a selected number of polymers. The present study focused on investigating the potential of using high-end engineering polymers in FDM. In addition, a critical review of the materials available on the market compared with those studied here was completed. Methods: Different engineering thermoplastics, ranging from industrial grade polycarbonates to novel polyetheretherketones (PEEKs), were processed by FDM. Prior to this, for innovative filaments based on PEEK, extrusion processing was carried out. Mechanical properties (i.e., tensile and flexural) were investigated for each extruded material. An industrial-type FDM machine (Stratasys Fortus® 400 mc) was used to fully characterize the effect of printing parameters on the mechanical properties of polycarbonate. The obtained properties were compared with samples obtained by injection molding. Finally, FDM samples made of PEEK were also characterized and compared with those obtained by injection molding. Results: The effect of raster to raster air gap and raster angle on tensile and flexural properties of printed PC was evidenced; the potential of PEEK filaments, as novel FDM material, was highlighted in comparison to state of the art materials. Conclusions: Comparison with injection molded parts allowed to better understand FDM potential for functional applications. The study discussed pros and cons of the different materials. Finally, the development of novel PEEK filaments achieved important results offering a novel solution to the market when high mechanical and thermal properties are required.