Background: Food allergies are known to resolve over time, but there is little information on the natural history of food-induced anaphylaxis (FIA). Objective: This study aimed to evaluate the natural history of FIA in children and determine the factors that affect prognosis. Methods: Children with FIA who were followed up for at least 3 years, between 2010 and 2020, were included. Patients' families were contacted by telephone to question their child's tolerance status and invite them for reevaluation if uncertain. The patients were grouped as tolerant or persistent according to parent reports or reevaluation results. Logistic regression analysis was performed to determine the factors that affected persistence. Results: The study included 185 patients (62.2% boys) with 243 anaphylactic reactions to various foods. Fifty-eight patients (31%) gained tolerance within a 3-year follow-up period. Tolerance rates were higher in patients with FIA to milk (40%) and egg (43.9%) compared with to tree nuts (18.8%), legumes (5.6%), and/or seafood (11.1%) (p < 0.001). In a multivariate analysis, risk factors for persistent FIA were multiple food anaphylaxis (odds ratio [OR] 3.755 [95% confidence interval {CI}, 1.134-12.431]; p = 0.030), total IgE > 100 kU/L (OR 5.786 [95% CI, 2.065-16.207]; p = 0.001), and skin-prick test wheal size > 10 mm (OR 4.569 [95% CI, 1.395-14.964]; p = 0.012) at presentation. Conclusion: Approximately a third of the patients with FIA developed tolerance within 3 years. Clinicians should remember that children with food allergies, even anaphylaxis, may develop tolerance over time. Regular follow up and reevaluation of tolerance status are necessary to avoid unnecessary elimination.