Abstract Introduction In the last decade, Venezuela suffers a humanitarian crisis, leading to massive emigration to border countries, including Colombia. One of the most vulnerable migrant groups is pregnant women. They face social and economic challenges, in addition to the barriers to access public health care services. These circumstances might increase adverse perinatal outcomes. This study aims to analyse the perinatal outcomes of Venezuelan migrants in Colombia and determine if the migration factor impacts on the perinatal results. Methods Data were obtained from the 2017 Colombian national birth register (n = 1,085 births in Venezuelan migrants and n = 654,829 in Colombian women). The premature birth (PB), low birth weight (LBW), 1-minute, and 5-minute Apgar score were compared to identify any association with the demographic, obstetric and neonatal characteristics, considering motheŕs origin as the primary exposure variable. Logistic regression models were used for the binary outcomes and linear regression models for continuous outcomes. Results The main difference was found in the low prevalence in health insurance coverage among Venezuelan women in comparison to natives (2.5% vs. 86.4%), and antenatal care visits (Mean 3.35±2.60 vs. 6.37±2.56). Venezuelan women were more likely to have newborns with LBW (OR 1.27; 95%CI 1.01, 1.58), lower Apgar scores at 1-minute (ß -0.09; 95%CI -0.14, -0.025) and 5-minute (ß -0.13; 95%CI -0.17, -0.08) in comparison to Colombians. Conclusions Our findings support that some neonatal outcomes among the Venezuelan migrants differed significantly from those of the Colombian women. The disadvantages found in health insurance coverage and antenatal care among migrants group were considered influencing factors. More effort among public health policies is needed to allow the migrant population having effective access to health care services, in order to improve the conditions of these women and their offspring. Key messages Pregnant migrant women are a vulnerable group in Colombia, facing health access barriers with neonatal consequences. The action is required by the application and reinforces of inclusive health policies among migrant population in Colombia.