Due to their susceptibilities, neonates and infants face unique SARS-CoV-2 challenges. This retrospective study will compare the illness course, symptoms, biomarkers, and lung damage in neonates and infants with SARS-CoV-2 infection from February 2020 to October 2023. This study was conducted at two hospitals in Timisoara, Romania, using real-time multiplex PCR to diagnose and lung ultrasonography (LUS) to assess lung involvement. Neonates had a more severe clinical presentation, an increased immune response, and greater lung involvement. Neonates had more PCR-positive tests (p = 0.0089) and longer hospital stays (p = 0.0002). In neonates, LDH, CRP, and ferritin levels were higher, indicating a stronger inflammatory response. Reduced oxygen saturation in neonates indicates respiratory dysfunction. The symptoms were varied. Infants had fever, cough, and rhinorrhea, while neonates had psychomotor agitation, acute dehydration syndrome, and candidiasis. This study emphasizes individualized care and close monitoring for neonatal SARS-CoV-2 infections. Newborn lung ultrasonography showed different variances and severity levels, emphasizing the need for targeted surveillance and therapy. Newborns have high lung ultrasound scores (LUSS), indicating significant lung involvement. Both groups had initial lung involvement, but understanding these modest differences is crucial to improving care for these vulnerable populations.