Independent lung ventilation (ILV) is a life-saving procedure in unilateral pulmonary pathologies. ILV is underused in clinical practice, mostly due to the technically demanding placement of a double lumen endotracheal tube (ETT). Moreover, the determination of ventilation parameters for each lung in vivo is limited. In recent years, the development of 3D printing techniques enabled the production of highly accurate physical models of anatomical structures used for in vitro research, considering the high risk of in vivo studies. The purpose of this study was to assess the influence of double-lumen ETT on the gas transport and mixing in the anatomically accurate 3D-printed model of the bronchial tree, with lung lobes of different compliances, using various ventilation modes. The bronchial tree was obtained from Respiratory Drug Delivery (RDD Online, Richmond, VA, USA), processed and printed by a dual extruder FFF 3D printer. The test system was also composed of left side double-lumen endotracheal tube, Siemens Test Lung 190 and anesthetic breathing bag (as lobes). Pressure and flow measurements were taken at the outlets of the secondary bronchus. The measured resistance increased six times in the presence of double-lumen ETT. Differences between the flow distribution to the less and more compliant lobe were more significant for the airways with double-lumen ETT. The ability to predict the actual flow distribution in model airways is necessary to conduct effective ILV in clinical conditions.