Neonatal lupus erythematosus (NLE) is a rare autoimmune disorder associated with transplacental migration of maternal autoantibodies against SS-A (Ro) or SS-B (La) antigens that results in cardiac, hepatic, cutaneous, and hematologic manifestations. Although NLE-associated neutropenia is considered transient and benign, neutropenia caused by severe congenital neutropenia (SCN) is life-threatening. Diagnosing a complicated picture of neonatal neutropenia can be challenging because there are many overlapping features between the acquired and inherited etiologies. This article highlights this diagnostic challenge with a case of delayed diagnosis of SCN due to an initial diagnosis of concurrent NLE. Secondary to SCN refractory to granulocyte colony-stimulating factor, our patient underwent a matched sibling cord blood transplant. Posttransplant, the patient developed recurrence of NLE symptoms, representing the first case of maternally transferred autoantibodies causing symptoms in a cord blood recipient. This novel finding prompted a review of the standards for collecting, processing, and storing of cord blood donations. This article also discusses the importance of physician familiarity with the differences and similarities between publicly and privately banked cord blood donations to adequately counsel expectant parents.