Objective: The purpose of this study was to compare the efficacy of different irrigation protocols on smear layer removal in root canals of primary teeth by scanning electron microscopy (SEM). Material and methods: The study was conducted with 40 extracted maxillary primary incisor teeth divided into four groups (n = 10) as 1% sodium hypochlorite (NaOCl), 10% ethylenediaminetetraacetic acid (EDTA)+1% NaOCl, 6% citric acid (CA)+1% NaOCl, and 0.9% physiological saline (PS). After the irrigation procedures, root canal walls were examined by SEM and the efficacies of irrigation solutions in smear layer removal were scored and compared. Data were analyzed using Kruskal-Wallis, Friedman and Siegel Castellan tests. Results: The smear layer removal was found to be statistically more effective in groups of 10% EDTA + 1% NaOCl and 6% CA + 1% NaOCl when compared with the other groups (p < .05). Smear removal efficacy was statistically significantly higher in coronal and medium thirds when compared with the apical regions in the experimental groups. Conclusions: It was concluded that 10% EDTA + 1% NaOCl and 6% CA + 1% NaOCl could be alternative irrigation protocols regarding smear layer removal. However, due to the absence of erosive dentinal changes, it might be suggested that using 6% CA + 1% NaOCl can be recommended compared to 10% EDTA + 1% NaOCl in primary root canals.