Fused filament fabrication (FFF) offers great potential to fabricate patient‐specific implants to treat large size defects resulting from craniectomy. Such cranial implants impose critical requirements on material and design. So far, the field has focused on printing cranial implants from polyetheretherketone (PEEK), which is semicrystalline in nature and, therefore, not ideal for FFF because of warping and nonhomogeneous crystallization. Consequently, this work aims at exploring alternative amorphous high‐performance polymers. The tensile and flexural mechanical properties of printed samples from PEEK, polyetherketoneketone (PEKK), and polyphenylsulfone (PPSU) according to ISO standards are compared. Testing of specimens obtained from three orthogonal build directions reveals nearly isotropic mechanical behavior (e.g. ultimate tensile strength differed no more than 8% between print orientations). This enables printing of patient‐specific cranial implants in vertical orientation with minimal support structures, which result in dimensional accuracies in the clinically acceptable range for craniofacial reconstructions. Mechanical assessment via an in‐house designed indentation set‐up shows that both PEKK and PPSU should be considered valid alternatives to PEEK for cranial implants. This work showcases the maturity of FFF for high‐performance polymers and leverages it for complex patient‐specific geometries such as a cranial implant.