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In recent decades, the number of pediatric transplantations and their survival rates have increased. Psychological problems and poorer quality of life are notable among children undergoing transplantation and can have long-lasting consequences and affect immunosuppressive therapy adherence. Pet ownership and animal contact have been associated with physical, mental, and social health benefits. Despite these potential benefits, however, companion animals are known to be a source of infection, which is one of the main concerns for clinicians. Because of immunosuppression, these children are particularly vulnerable to infections. Zoonoses comprise a long list of infectious diseases and represent a major public health problem. Nevertheless, many families and most healthcare providers are unaware of these potential risks, and there is a worrisome lack of recommendations to manage the risk-benefit balance, which could pose a risk for acquiring a zoonosis. Furthermore, no data are available on the number of transplanted patients with pets, and this risk-benefit balance is difficult to adequately evaluate. In this document, we review the currently available evidence regarding the epidemiology of zoonotic infections in patients undergoing transplantation, focusing on pediatric patients from a risk-benefit perspective, to help inform decision-making for clinicians. Families and healthcare professionals should be aware of the risks, and clinicians should actively screen for pets and offer comprehensive information as part of routine clinical practice. A multidisciplinary approach will ensure proper care of patients and pets and will establish preventive measures to ensure patients are safe living with their pets.