The COVID-19 epidemic is a major public health emergency that has affected every part of society worldwide, including neonates with different clinical presentations. It is essential to differentiate between increased incidence of complications related to this infection rather than an underlying congenital etiology. We report a rare case with atypical lung cystic lesions, diagnosed initially as congenital pulmonary airway malformation (CPAM) with management controversy but which turned out to be a COVID-19 viral pneumonia complication. Clinical tolerance and proper uses of radiological modalities are crucial to achieving better outcomes for patients. The literature is still missing reports on this topic and needs more studies to provide conclusive, evidence-based practice of this emerging neonatal viral infection. Vigilance in neonates with COVID-19 infection is highly recommended.