Introduction Maternal and neonatal tetanus remains a global public health problem affecting mainly the poorest and most marginalized subpopulations. In spite of the problem, studies conducted on the associated factors of births protected against neonatal tetanus are scarce in Africa. Therefore, this study aimed to identify both individual and community-level factors associated with births protected against neonatal tetanus in the region. Methods The most recent Demographic and Health Survey datasets of five African countries (Ethiopia, Burundi, Comoros, Zimbabwe and Zambia) were used to investigate the associated factors of births protected from neonatal tetanus. STATA Version 14 statistical software was used for the analysis. The data were weighted before doing any statistical analysis and deviance was used for model comparison. Multilevel binary logistic regression was used to identify the associated factors of births protected against neonatal tetanus. Finally, the adjusted odds ratio (AOR) with its 95% confidence interval (CI) was calculated for each potential factors included in the multivariable multilevel logistic regression model. Results A total weighted sample of 30897 reproductive age women who had a birth within 5 years preceding the survey were included in the analysis. Those women with age of 20–34 (AOR = 1.32, 95%CI: 1.18–1.48) and 35–49 years (AOR = 1.26, 95% CI: 1.10–1.44), high community level of women education (AOR = 1.13, 95%CI: 1.04–1.23), being from poorer(AOR = 1.23, 95% CI: 1.14–1.33), middle (AOR = 1.31, 95%CI: 1.21–1.43), richer (AOR = 1.21, 95%CI: 1.11–1.32) and richest households (AOR = 1.59, 95%CI: 1.44–1.74), having antenatal care follow up (AOR = 9.62, 95% CI: 8.79–10.54), not perceiving distance to health facility as a big problem (AOR = 1.18, 95% CI: (1.11–1.25) had higher odds of having births protected against neonatal tetanus. Conclusion Both individual and community level factors were found to be associated with births protected against neonatal tetanus in Africa. This suggests that a variety of factors are affecting births protected against neonatal tetanus in the region. Hence, the impact of these factors should be recognized while developing strategies to reduce neonatal tetanus in the region.