Objective: This study aimed to compare the EndoVac system and conventional needle irrigation in removing smear layer (SR) from primary molar root canals. Materials and Methods: Fifty extracted human primary second molar roots were instrumented up to an apical size of 0.04/35 and randomly divided into two main groups; Group 1: EndoVac system (n = 25) and Group 2: Conventional needle irrigation (n = 25) and three subgroups (a) NaOCl + ethylenediaminetetraacetic acid (EDTA) (n = 20) (b) ozonated water (OW) + EDTA (n = 20) and (c) saline (control, n = 10). After a standardized final irrigation protocol performed for all teeth, scanning electron microscope images were taken at x1000 magnification for each thirds of each root canal. Data were analyzed by the weighted kappa, Kruskal-Wallis, and Wilcoxon signed rank tests. Results: EndoVac was more effective than conventional needle in the removal of SR from the apical third of the root canal system (P < 0.05). The OW + EDTA regimen provided similar SR removal compared with NaOCl + EDTA. Conclusions: EndoVac has better performance than conventional needle irrigation in the removal of the SR in the apical thirds of the primary molar root canals. As a final irrigation regimen, the OW + EDTA regimen is as effective as the NaOCl + EDTA regimen.