Background Malnutrition in pregnancy remains unacceptably high across all regions of Africa though promising progresses have been made globally. Primary studies might not be sufficient to portrait a comprehensive picture of malnutrition during pregnancy and its main risk factors. Therefore, we intended to review the burden of malnutrition, for this specific review implies to protein energy malnutrition, during pregnancy in Africa to present its magnitude and determinant factors. Methods We did a systematic review of observational studies published from January 1/2008 to January 31/2018. The CINAHL(EBSCO), MEDLINE (via Ovid), Emcare, PubMed databases and Google scholar were searched. Articles quality was assessed using the Newcastle-Ottawa Scale and studies with fair to good quality were included. We pooled malnutrition prevalence and an odds ratio estimates for risk factors after checking for heterogeneity and publication bias. This review has been registered in Prospero with a protocol number CRD42018114949. Result 23 studies involving 20,672 pregnant women were included. Using a random effect model, the overall pooled prevalence of malnutrition among pregnant women in Africa was 23.5% (95%CI: 17.72-29.32; I2 = 98.5%). Based on the current review pooled odds ratio finding; rural residency (POR = 2.6%; 95%CI: 1.48-4.65; I2 = 0%), low educational status of partners (POR = 1.7%; 95%CI: 1.19-2.53; I2 = 54.8%), multiple pregnancy (POR = 2.15%; 95% CI: 1.27-3.64; I2 = 0%) and poor nutritional indicators (POR = 2.03%; 95%CI: 1.72-2.4, I2 = 0%) were positively determine maternal malnutrition. On contrary, better household economic status (POR = 0.47%; 95%CI: 0.36-0.62; I2 = 24.2%) negatively determine maternal malnutrition. Conclusion A significant number of the pregnant population in Africa are suffering of malnutrition, above 10% of the standard acceptable malnutrition rate. Thus, efforts should be renewed to ensure a proper and widespread implementation of programs that would address issues identified in the current review to reduce the burden of malnutrition.