We present a patient with multiple pigmented lesions on the palms, soles, oral mucosa and nails after chemotherapy with oral 5-fluorouracil (5-FU) prodrug. Dermoscopically, most of the macules showed similar features, with pigmentation present predominantly on the crista superficialis, while a large, dark macule also showed pigmentation along the sulcus superficialis with irregular hyperpigmentation and depigmentation, suggesting malignancy. However, histologically, both types of lesion showed basal hyperpigmentation and the presence of a small number of large atypical melanocytes. We diagnosed these lesions as pigment flecks induced by 5-FU, and the pigmented lesions gradually diminished after the cessation of chemotherapy. Our findings suggested that immunosuppression and 5-FU led to the development of the atypical pigmented lesions.