Alopecia areata (AA) is a chronic inflammatory disease that causes partial or complete hair loss and is based on autoimmune processes. Current studies are actively investigating the use of JAK inhibitors for AA treatment, but data on the safety and efficacy of these drugs in patients with congenital immunodeficiency are practically non-existent. A unique clinical case of familial form of severe AA in two sisters with congenital immune disorders, that caused certain difficulties in treatment, is presented. The older sister, 24 years old, has been diagnosed with primary immunodeficiency — selective IgA deficiency combined with IgG2 deficiency, and the younger sister, 18 years old, is under observation with suspicion of immunodeficiency with a predominant defect of antibodies. Both patients receive targeted therapy with tofacitinib, in presence of which a partial hair regeneration, more pronounced in the younger sister, has been noted. This clinical case emphasizes the need for multidisciplinary interaction of dermatologists, immunologists and geneticists in treating patients with AA and congenital immune disorders. Special attention should be paid to clinical and laboratory monitoring to minimize the risk of infections associated with therapy using JAK inhibitors. Our observation contributes to the understanding of genetic and immune mechanisms of AA and confirms the possibility of JAK inhibitors application in patients with autoimmune diseases affected by immunodeficiency. These data may serve as an addition to the development of new recommendations and treatment algorithms in such cases, and still the final efficacy and safety of such therapy require further study.