Background: Cow’s milk allergy (CMA) and cow’s milk intolerance (CMI) are the major cow’s milk disorders observed in infants and young children. This study investigates, for the first time, physician knowledge regarding CMA and CMI prevalence, diagnosis, and management in the Middle East and North Africa (MENA) region. In addition, we explore the role of goat milk-based formula as an alternative in infants suffering from CMI. Method: This cross-sectional survey was conducted from December 2020 to February 2021. A convenience sample of 2500 MENA-based physicians received the questionnaire, developed by a working group of pediatric experts. Results: 1868 physicians completed the questionnaire, including pediatric specialists (80.8%), training physicians (0.2%), dermatologists (0.1%), family/general physicians (12.9%), neonatologists (3.6%), neurosurgeons (0.2%), allergy nurse specialists (0.3%), pharmacists (2.1%), and public health workers (0.1%). Differentiation between CMA and CMI was recognized by the majority of respondents (80.7%), for which the majority of respondents (35.4%) identified that the elimination and challenge test was the best test to differentiate CMA from CMI, whereas 30.7% and 5.4% preferred the immunoglobulin E (IgE) test and skin prick test, respectively. In addition, 28.5% of respondents reported that there is no confirmatory test to differentiate CMA from CMI. The majority of respondents (47.3%) reported that amino acid-based formula (AAF)/ extensively hydrolyzed formula (EHF) is the cornerstone for the management of CMA. However, most respondents (33.7%) reported that lactose avoidance was best for the management of CMI. Overall, 65% of the respondents were aware of nutritionally adapted goat’s milk formula as an alternative to cow’s milk products and 37% would recommend its routine use in infants (≤2 years of age). Conclusion: The results of this survey demonstrate that the majority of physicians are aware of the underlying pathophysiology and management of CMA and CMI. However, a significant proportion of physicians do not follow the clinical guidelines concerning CMA/CMI diagnosis and management. Notably, this survey identified that goat’s milk formulas may offer a suitable alternative to AAF/EHF in infants with CMI as they contain β-casein protein which is easily digestible. In addition, goat’s milk formulas contain higher levels of oligosaccharides and medium-chained fatty acids compared with standard cow’s milk formulas, yet further clinical trials are warranted to support the inclusion of goat’s milk formulas in clinical guidelines.