Cutaneous lesions in Whipple disease (WD) are infrequent, and the histological findings are usually nonspecific. Specific cutaneous lesions have rarely been described and usually involve the subcutaneous fat. We report a patient diagnosed with WD, who developed multiple small subcutaneous nodules after antibiotic treatment was administered. In addition to septal panniculitis, the cutaneous biopsy showed a mild granulomatous dermal reaction with PAS-positive macrophages characteristic of WD. A positive polymerase chain reaction in the cutaneous sample confirmed the presence of Tropheryma whipplei in the skin. Dermatopathologists should be aware that not only subcutaneous lesions but also dermal lesions may exhibit specific findings of WD.