Objectives: The objective of this study is to compare the efficacy of chitosan (CS) nanoparticles (CNPs), citric acid (CA), and ethylenediaminetetraacetic acid (EDTA) in removing the smear layer using two different irrigation needles. Materials and Methods: Palatal roots of 70 maxillary first molars were decoronated, instrumented, and divided into four experimental groups ( n = 20) and one control group ( n = 10). The groups received a final rinse of 0.5% CNPs, 10% CA, 17% EDTA, and distilled water for 3 min. Every group was subdivided into two subsections: IrriFlex ® endodontic or ProRinse ® irrigation needles. Specimens were divided lengthwise and viewed under a scanning electron microscope for evaluation. Statistical Analysis Used: Nonparametric Kruskal–Wallis and Mann–Whitney U -tests were used to compare the results ( P < 0.05). Results: CNPs were as efficient as CA and EDTA as a chelating agent. However, significantly more efficient apically. At all three levels, there was no significant difference between A1 and A2. At the coronal and middle levels, there was a significant difference between B1 and B2, as well as apically between C1 and C2. Conclusions: CNPs remove the smear layer with the same efficiency as other irrigants utilized in this study at coronal and middle levels and more efficiently at the apical levels. IrriFlex ® was more effective than ProRinse ® in removing the smear layer when used with EDTA and CA, while there was no difference when used with CNPs.