Background: Danger signs in the neonatal period are non-specific and could be a manifestation of almost any newborn disease. Early recognition of these signs by mothers is a pre-request for increasing neonatal care-seeking behavior. There four this study aimed to assess knowledge of neonatal danger signs and associated factors among mothers who gave birth at home and health institutions in Meicha District, Northwest Ethiopia. Methods: A community based comparative cross-sectional study was conducted among Home and Health institutions delivered mothers two months before the survey. A simple random sampling method was used to select the participants. Data was collected by face to face interviews of mothers. Binary logistic regression analysis was used to identify associated factors. The odds ratio with 95% CI was computed to assess the strength of the associations. Result: A total of 650 (325 health institution delivered and 325 home delivered) mothers were interviewed. Among this, 50.7% (AOR=2.19, 95%, CI (1.594-3.003)) of the mother were knowledge of neonatal danger sign in the district. Mother knowledge of neonatal danger sign was higher among mothers who give birth health institution (60.1%) than home (41.1%). Age of the mother (AOR:3.99, 95% CI:(1.45-11.03)), age of new born (AOR:0.53, 95% CI:(0.36-0.78)), parity (AOR:1.27, 95% CI:(1.37-5.31)), postnatal care attendance (AOR=2.42,95% CI: (1.47, 3.96)), distance of health center (AOR:0.46,95% CI:(0.27,0.78)) were significantly associated with overall mother’s knowledge of neonatal danger sign. Whereas, residence (AOR: 3.09, 95% CI:(1.44, 6.64)) and occupational status of husband (AOR:0.23, 95% CI:(0.201,0.67)) were significantly associated with health institution delivered mother. Age of new born (AOR: 0.50, 95% CI:(0.28,0.896)), parity(AOR: 0.29, 95% CI:(0.113,0.74)), antenatal care (AOR: 12.04, 95% CI: (5.9,24.65)) and postnatal care attendance (AOR:0.27,95% CI:(0.138,0.51)) was significantly associated with home delivered mother. Conclusion: The overall mother’s knowledge of neonatal danger signs was low. However, health institutions delivered mother more knowledge about danger signs than home-delivered mothers. Therefore, it is better if the district Health Office should investigate the implementation of educational programs in the community and strengthen the health extension program.