Cortical lesions (CLs) detected with double inversion recovery (DIR) magnetic resonance imaging (MRI) are very helpful in differentiating multiple sclerosis (MS) from other neuroinflammatory diseases of the central nervous system (CNS), that is, neuromyelitis optica spectrum disorders (NMOSDs). Furthermore, CLs are closely related to motor and cognitive impairment. We report a case of a 48-year-old female MS patient who developed several CLs during anti-CD20 therapy. Some CLs disappeared during follow-up MRIs. In the suspicion of a treatment failure, the screening for the autologous hematopoietic stem cell transplant (AHSCT) was performed with the evidence of an atrial myxoma. In MS patients with new CLs, a comorbid ischemic pathology should be considered and carefully investigated.