We herein report a woman in her 50s with systemic lupus erythematosus (SLE) who developed swelling and pain in her fingers; the symptoms were more prominent in winter. Magnetic resonance imaging (MRI) revealed bone edema in the phalanges of both hands, which was compatible with phalangeal microgeodic syndrome (PMS). This is the first reported case of PMS in a patient with SLE and suggests that performing MRI should be considered for patients with SLE in order to assess the nature of finger symptoms and signs more precisely.