To evaluate the effect of immersion in 3% sodium hypochlorite solution in the resistance to cyclic fatigue of three nickel-titanium (NiTi) rotary file systems, ProTaper Next (PTN), Hyflex CM (CM), and Hyflex EDM (EDM), in a mechanical model featuring axial movement. Ninety instruments of three different NiTi rotary file systems, PTN (size 25, 0.06 taper), CM (25, 0.06), and EDM (25/~, variable taper), were randomly divided according to a 3 × 3 factorial design and tested under dynamic immersion in a 3% NaOCl solution (1 or 5 min) or without immersion, making a total of 9 groups (n = 10). Files were tested in an artificial root canal with 45° angle and 5 mm radius apical curvature being submitted to back-and-forth movements until fracture. Statistical analysis was performed using two-way factorial ANOVA with Bonferroni post-hoc tests, at a significance level of 5%. Instruments were evaluated for reliability using a Weilbull approach. Regardless of the immersion treatment, PTN had on average 1200 ± 178 cycles to fracture, CM had 1949 ± 362, and EDM had 5573 ± 853, which was a significantly different (P < 0.01). The NaOCl immersion promoted a significant reduction in the mean number of cycles to fracture (P = 0.01), and was reflected in a significant reduction of the characteristic life of the instruments of the CM end EDM groups. Within this study conditions, EDM instruments performed better to cyclic fatigue followed by CM and then PTN. Immersion in NaOCl decreased the resistance to cyclic fatigue of all tested instruments, but affected more those manufactured from CM wire.