The aim of this work was to study the properties of polylatic acid/polyamide 11 (PLA/PA11) blends compatibilized with a multifunctionalized epoxide, Joncryl^®, and to evaluate the performance of such blends processed by Fused Deposition Modeling (FDM) 3D printing, compared to those produced by injection molding method. Blends containing different Joncryl contents from 0.5 to 3 wt% were prepared by twin-screw extrusion. Evaluation of thermal, rheological and mechanical properties of such blends proved that Joncryl acted as a compatibilizer. Results showed that Joncryl effects on blends properties were improved with increasing its content. A significant reduction of PA11 dispersed phases diameter and an improvement of tensile properties with a ductile behavior were achieved for the highest Joncryl contents. A significant elongation of PA11 dispersed phases was observed into FDM filaments and dog bone shaped specimens produced thereafter. Despite this peculiar morphology, FDM printed samples exhibited only enhanced stiffness but poor reinforcement and elongation at break in comparison with injected ones.