The rare presence of proliferative nodules in cases of giant congenital naevus can, in some cases, be potentially misdiagnosed as neonatal melanoma. We report here a case of multiple, proliferative nodules found in a giant congenital naevus lesion in a female neonatal patient diagnosed with neurocutaneous melanosis. Our initial clinical observations of this case suggested the possibility of primary cutaneous neonatal melanoma or skin metastasis from a melanoma in the meninges or elsewhere in the central nervous system. However, histological examination revealed no sign of melanoma, abnormal mitosis, necrosis or any malignant change. Pagetoid arrays of naevus cells in the junctional zone and myxoid changes present in a significant portion of the dermis led to the diagnosis of proliferative nodules. Distinct histological patterns seen in the proliferative nodules in our neonatal patient were useful to differentiate between benign pigmented nodular lesions in a giant congenital naevus and malignant melanoma, and reduced the chance of misdiagnosis.