Introduction The severity of coronavirus disease 2019 in neonates was variable. Studies describing the morbidities in neonates due to coronavirus disease 2019 among outborn neonates were limited. The impact of maternal immune status due to vaccination against coronavirus disease in 2019 on neonates remains unexplored. Hence, we aimed to compare the clinical profile of coronavirus disease 2019 among outborn neonates during the different waves. Materials and Methods We did a medical record-based retrospective study of neonates with coronavirus disease 2019 admitted between January 2020 and July 2022 in a tertiary care out-born neonatal unit in India. They were stratified based on the period of admission into the first, second, and third waves. Outcome variables, including demographic, clinical, laboratory, radiological, and treatment data of the eligible neonates, were obtained and compared between different waves. Results Among the 32 neonates enrolled, 17 were admitted during the first wave, 15 during the second wave, and none during the third wave. Of all, 24 (75%) neonates were symptomatic. Contact with coronavirus disease 2019-positive mothers and the occurrence of fever and lethargy were high during the second wave. Inflammatory markers were elevated in 12 (46%), and 28% had abnormal X-rays. Eight (25%) neonates required respiratory support, and five (16%) required mechanical ventilation. The clinical outcome was good, with 91% being discharged home. No significant difference in demographics, laboratory markers, mode of treatment, or clinical outcome between the first and second waves was identified. Conclusions Transmissibility from coronavirus disease 2019-positive mothers to neonates was high during the second wave, with more coronavirus disease 2019-related symptoms. Symptomatic neonates were milder in severity but improved with supportive care.