Objectives: To find out the early neonatal outcome (morbidity and early neonatal mortality) of the babies born by caesarean section (CS) and to compare the outcomes between elective and emergency CS. Methods: A longitudinal study was conducted in a tertiary care hospital. Maternal and neonatal characteristics were noted. Results: A total of 750 neonates were enrolled and 37% were born by elective CS. Out of 750 children 55% were male newborns and 45% were females. The NICU (neonatal intensive care unit) admission requirement was 24%, whereas 3.33% of neonates died within 7 days of life. Neonatal morbidity was higher in emergency CS, similar to respiratory depression at birth (OR: 6.00, 95% CI 3.06-11.78, P < 0.001), respiratory distress (OR: 4.6, 95% CI 2.74 -7.82, P < 0.001) and requirement of resuscitation (OR: 5.54, 95% CI 2.98 -10.32, P < 0.001). Factors such as emergency CS [adj OR: 13.35(1.69 -105.38), P = 0.014], prematurity .47), P < 0.001] and Apgar score < 7 at 10 minutes .50), P < 0.001] were independently associated with NICU admissions and neonatal mortality. Conclusions: Newborns delivered through emergency CS had a higher morbidity and mortality rate compared to elective CS. Adequate antenatal care and early referral may convert this emergency CS to normal or elective CS and can reduce neonatal morbidity and mortality.