Prader-Willi Syndrome (PWS) is a rare genetic disorder resulting from the absence of expression of genes in the 15q11–q13 region on the paternally derived chromosome 15. The present case report describes the chromosomal anomalies suspected to be present in a neonate, detected using Chromosomal Microarray analysis, an advanced platform for genetic analysis. Whole blood sample of the patient was analysed to reveal a pathogenic deletion spanning the region 15q11.2–q13.3; a rare and extended deletion involving breakpoints BP1 to BP5. The identification of this atypical deletion underscores the importance of precise genetic characterization in PWS diagnosis. Early detection through cutting-edge genetic testing enables timely intervention and management of associated abnormalities, highlighting the significance of integrating advanced genomic analysis into clinical practice. The current study contributes to the growing understanding of PWS genetics and emphasizes the need for comprehensive genetic evaluation in patients with suspected PWS.