Bacterial and fungal pathogens in recirculating aquaculture and egg incubation systems can cause elevated mortality and decreased production. Peracetic acid (PAA) is a relatively low‐cost, safe, and effective disinfectant; however, its toxicity to early life stages of the Atlantic salmon (Salmo salar) has not been assessed. The 24‐h LC50 value of PAA was determined for three early life stages of Atlantic salmon: eyed eggs, fry (~0.17 g), and fingerlings (~16.3 g). LC50 values were calculated using the Trimmed Spearman‐Karber (TSK) method and Toxicity Relationship Analysis Program (TRAP). TRAP LC50 values for eyed eggs treated for 5 and 10 min were 781.5 and 485.0 mg/L PAA, respectively, while TSK LC50 values for eyed eggs treated for 5 and 10 min were 771.1 and 462.1 mg/L PAA, respectively. TRAP LC50 values for fry and fingerlings were 4.0 and 5.3 mg/L PAA, respectively, while TSK LC50 values for fry and fingerling were 4.1 and 5.3 mg/L PAA, respectively. The no observed effect concentration (NOEC) values for eyed eggs treated for 5 and 10 min were 500 and 300 mg/L PAA, respectively. These LC50 and NOEC values provide guidance for developing safe PAA treatment protocols Atlantic salmon eggs, fry, and/or fingerlings.