Atopic dermatitis (AD) is the most common chronic skin disease in children, with an increasing prevalence in the past three decades. Adequate treatment is prescribed for individual patient based on symptoms and disease severity. However, further underlying diagnosis should be researched when therapeutic strategies for symptoms fail and skin lesions and pruritus persist. We reported herein the case of a 19-month-old infant with a history of AD unresponsive to treatment due to the type 2 progressive familial intrahepatic cholestasis (PFIC). A new homozygous mutation of the ABCB11 gene was found. The severe pruritus, the early onset jaundice, poor growth and raised transaminase levels with normal gamma glutamyl transpeptidase have led to the suspicion of PFIC. The presence of severe AD and intrahepatic chronic cholestasis, both pruritus associated, could delay a proper diagnosis. To our knowledge, for the first time, a case of comorbidity between type 2 PFIC and AD-like disease had been described.