Abstract: Severe forms of atopic dermatitis (AD) cause significant morbidity in vulnerable pediatric populations and necessitate treatment with systemic therapy. The existing literature concerning the treatment of severe pediatric AD with azathioprine (AZ) and mycophenolate mofetil (MM) is sparse. The purpose of this case series is to examine the use of these two drugs in the treatment of severe pediatric AD. Medical records of 28 pediatric patients with AD from the University of North Carolina at Chapel Hill pediatric dermatology clinic treated using these two drugs were analyzed for laboratory values, thiopurine methyltransferase (TPMT) levels, symptoms, infections, and other relevant data. Patients were also contacted via the telephone to ascertain outcomes and any missing data. Treatment outcomes were scored into three categories: significant improvement, some improvement, and no improvement. AZ dosing was correlated to TPMT levels successfully, with comparable levels of improvement in the heterozygous and homozygous wild-type groups. Absolute eosinophil count corresponded to AD activity and treatment response across both treatment modalities in 18 of 26 (69%) patients. Seventeen of 28 (61%) patients treated with AZ and eight of 12 (66%) treated with MM reported significant improvement. We had lower rates of laboratory abnormalities and side effects with MM than with AZ but similar rates of cutaneous infections. Treatment outcomes did not appear to differ with race, sex, or TPMT level. We experienced success with AZ and MM in the treatment of severe pediatric AD. Coordinating treatment to each patient’s unique morbidities is the best way to choose systemic treatments.