Background: Approximately 50–90% of children with immediate-type cow’s milk allergy (CMA) acquire tolerance by pre-school age. We aimed to investigate the tolerance acquisition rate of CMA in children aged 6–12 years. Methods: Children with CMA that persisted until 6 years of age were included. Tolerance acquisition was defined as either passing an oral food challenge with 200 mL of unheated cow’s milk (CM) or consuming CM of any quantity without symptoms. Persistent CMA was defined as fulfilling neither of these criteria by 12 years of age. Children undergoing oral immunotherapy were defined as having persistent CMA. Risk factors associated with persistent CMA were assessed using Cox regression analysis. Results: Of the 123 children analyzed, 60 (49%) had previous CM anaphylaxis, 82 (67%) eliminated CM from their diet, and the median CM-specific immunoglobulin E (sIgE) level was 23.3 kU _A/L at 6 years of age. Twenty-five children (20%) acquired tolerance by 9 years of age, and 46 (37%) by age 12. At baseline, higher CM-sIgE levels (hazard ratio: 2.58 [95% confidence interval: 1.62–4.12], optimal cutoff level: 34.4 kU _A/L), previous CM anaphylaxis (2.42 [1.24–4.69]), and complete CM elimination (5.18 [2.45–10.99]) were associated with persistent CMA. None of the children with CMA who had all three risk factors (n = 26) acquired tolerance. Conclusion: At least one-third of the children with CMA at 6 years of age acquired tolerance by 12 years of age. Children with CMA who have the risk factors are less likely to acquire tolerance.