This article reports 3D printing of carbon nanotube‐polylactic acid (CNT‐PLA) composites using an extrusion‐based Fused Deposition Modeling (FDM) method. CNTs with an average diameter of 128 nm and an average length of 2.5 μm were first compounded with PLA and extruded into feedstock filaments at 0.5%, 2.5%, and 5% (w/w) CNT loadings. CNT aggregates were observed, but no clogging occurred during printing with a 500‐μm print nozzle. The rheology of the CNT‐PLA samples was characterized to understand the printing‐induced alignment of CNTs along the road axis. Additionally, the effect of printing flow rate was explored for a fixed printing gap and nozzle diameter. Higher flow rates reduced the void fraction in the FDM parts, but unexpectedly resulted in less degree of CNT alignment, which is attributed to radial flow and fusion between adjacent roads. The mechanical properties of the CNT‐PLA tensile test coupons were characterized. Inclusion of CNTs increased the Young's modulus by 30% at 5% CNT loading, but reduced the tensile strength and overall toughness of the FDM parts. Experimental data were compared against the Rule of Mixtures (RoM) model, the Halpin‐Tsai model, and the modified RoM model and were further explained by the void fraction and CNT orientation. POLYM. COMPOS., 39:E1060–E1071, 2018. © 2017 Society of Plastics Engineers