This case report presents a 7-year-old boy with severe, early-onset cow’s milk allergy (CMA) and poorly controlled, severe persistent asthma, highlighting the challenges of managing pediatric allergic multimorbidity. The patient experienced multiple anaphylactic reactions to cow’s milk, significantly impacting his quality of life. Despite adherence to conventional asthma therapies, his asthma remained poorly controlled. Given the severity of his condition and the underlying immunoglobulin E (IgE)-mediated inflammation, treatment with omalizumab, an anti-IgE monoclonal antibody, was initiated. Following omalizumab initiation, significant improvements were observed in asthma control, including reduced symptoms, improved pulmonary function, and decreased airway inflammation. Additionally, although a formal oral food challenge after five months of treatment elicited an anaphylactic reaction, the threshold dose triggering the reaction was significantly higher than previous reactions, indicating an increase in tolerance to cow’s milk proteins. This case underscores the potential of omalizumab in improving asthma control and increasing tolerance to cow’s milk, with associated benefits to the patient, but also highlights the variability in response when targeting co-existing allergic conditions. Further research is needed to optimize treatment strategies for pediatric allergic multimorbidity.