Background Stunting at birth is a chronic form of undernutrition majorly attributable to poor prenatal nutrition, which could persist in children's later life and impact their physical and cognitive health. Although multiple studies have been conducted in Ethiopia to show the magnitude of stunting and factors, all are concentrated on children aged between 6 to 59 months. Therefore, this study was done to determine the prevalence and associated factors of stunting at birth among newborns delivered at the University of Gondar Comprehensive Specialized Referral Hospital, Northwest, Ethiopia. Methods An institution-based cross-sectional study was conducted from February 26.sup.th to April 25.sup.th/ 2020. A systematic random sampling technique was used, to select a total of 422 newborn-mother pairs. The binary logistic regression was employed to identify factors associated with stunting and all independent variables were entered into the multivariable logistic regression model to adjust for confounders. Variables that had significant association were identified based on p-value Results About 30.5% (95% CI: 26.3%, 35.1%) of newborns were stunted at birth. Being male [Adjusted odds ratio (AOR) = 2.9(1.62, 5.21)], newborns conceived in Kiremt(rainy season) [AOR = 2.7(1.49, 4.97)], being low birth weight [AOR = 3.1(1.64, 6.06)] were factors associated with stunting at birth. Likewise, newborns born to short stature mothers [AOR = 2.8(1.21, 6.62)] and chronically malnourished mothers [AOR = 15.3(8.12, 29.1)] were at greater risk of being stunted. Conclusion Just under a third of newborns are stunted at birth, implying a pressing public health problem. Newborns born to chronically malnourished and short stature mothers were more stunted. Besides, stunting was prevalently observed among male neonates, newborns conceived in Kiremet, and being low birth weight. Thus, policymakers and nutrition programmers should work on preventing maternal undernutrition through nutrition education to reduce the burden of low birth weight and stunting. Further, paying due attention to newborns conceived in Kiremet season to improve nutritional status is recommended.