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Atopic dermatitis (AD) is a common chronic, pruritic skin disease in children. As the incidence of AD increases, especially in high-income countries, paediatricians may see an increasing number of recalcitrant AD cases in their practice. Although these cases are principally managed by paediatric dermatologists, it is important for paediatricians to be aware of the use and side effects of non-topical treatment like phototherapy and systemic agents as well as the evidence for alternative treatment, which caregivers may ask about. This review presents paediatric evidence for the practical use of phototherapy and certain oral immunosuppressants for paediatric AD including doses, duration of use and monitoring of adverse effects. The use of alternative therapy including traditional medicine, probiotics and the role of nutrition are also discussed. Narrow band ultraviolet B phototherapy is effective in recalcitrant paediatric AD. When phototherapy is ineffective or contraindicated, systemic drugs may be administered cautiously with close surveillance of side effects. The use of azathioprine, ciclosporin, methotrexate and mycophenolate mofetil is generally safe in the short term under close monitoring and can be effective alongside compliance to topical treatment. Alternative complementary treatment is not known to be effective. Holistic management including therapeutic patient education is important. Good quality paediatric studies for non-topical AD treatment are needed for definitive guidelines.