Polyetherketoneketone (PEKK) (60/40 TERE/ISO) is characterized by a lower processing temperature and a higher glass transition temperature (Tg) compared to polyetheretherketone (PEEK), making it a promising material for 3D printing. However, it remains in amorphous state post-printing due to its slow crystallization rate. In this study, isothermal annealing is conducted on 3D printed pseudo amorphous PEKK at various times and temperature. Thermal analysis techniques reveal that both annealing time and temperature play a pivotal role in enhancing crystallinity, with levels reaching up to 27% when annealed between the Tg and the melting temperature (Tm). However, thermal stability decreased as the annealing temperature approached Tm. X-ray diffraction studies demonstrate that annealing between Tg and Tm promotes the development of stable form II crystals, while annealing at higher temperatures encourages the formation of form I crystals. Furthermore, dynamic mechanical analysis indicated a 44% increase in mechanical stiffness following annealing, and compressive testing shows improved yield strength, comparable to that of other polyaryletherketone (PAEK) materials. These findings suggest that controlled annealing of 3D printed PEKK enables precise tailoring of its crystallinity and mechanical properties, making it adaptable for a wide range of applications, such as biomedical devices that require patient-specific customization.