Bowen’s disease (BD) is a non-melanoma skin cancer with several histological subtypes. Herein we describe a case of a 35-year-old woman with a 4-cm diameter crusted plaque on the parietal scalp region. She had the lesion for 2 years. It had previously been histologically diagnosed as pemphigus vulgaris and only treated with a topical cream. The lesion progressively became thicker and larger. A new biopsy showed atypical cell proliferation through the whole thickness of the epidermis and follicular epithelium, with dermal microinvasion along with acantholysis and clear cell formation. The patient underwent total lesion excision (1 cm margin) with the diagnosis of both acantholytic and pagetoid subtypes of BD and dermal microinvasion. We describe a rare case of a young female patient with both subtypes of BD present in one lesion on an area not exposed to the sunlight. The lesion was initially misdiagnosed as pemphigus vulgaris.