This study describes a detailed analytical characterization of polyaryletherketone (PAEK) polymers used in extrusion‐based additive manufacturing. The results provide key observations and highlight differences between commercially available polymers of the PAEK family, specifically polyetheretherketone (PEEK) and polyetherketoneketone (PEKK). Results suggest that inherent differences in their molecular structure lead to notable differences in terms of their viscoelastic, thermal and physical properties. Similarly, direct comparison of the properties between parent filaments and three‐dimensional printed (3DP) parts suggests that, as observed in subtractive processes, the molecular structure of the PAEK polymer selected (PEEK or PEKK), as well as the inherent physical properties associated with it, determine greatly the performance of final 3DP parts. Differential scanning calorimetry results suggest that the glass transition temperature (Tg) of PEEK 3DP bars (146.8 °C) is about 8 °C lower than that of the parent PEEK filament (154.8 °C). These small differences manifest greatly in the viscoelastic response after Tg, and the temperature at which a decrease in storage modulus is observed occurs consistently at lower temperatures in 3DP PEEK bars (ca 130 °C) compared to PEEK filaments (ca 150 °C). In contrast, no observable differences are noted between parent filaments and 3DP bars in PEKK polymers. For these polymers, the inherent semi‐crystalline behavior dominates their thermal and viscoelastic response. These structure–property relationships provide fundamental understanding to aid in the design and manufacturing of several industrial and biomedical applications that could potentially leverage the advantages of high‐temperature thermoplastic PAEK resins, as well as in the incorporation of these polymers in a growing number of technologies encompassing the field of additive manufacturing. © 2021 Society of Industrial Chemistry.