Breast milk is one of the many distinct forms of food that can be contaminated with aflatoxin M1 (AFM1). They may be consumed by eating contaminated foods, such as contaminated meat and crops, which would then be present in breast milk and cause health problems, including nervous system disorders and cancers of the lungs, liver, kidneys, and urinary tract. However, the prevalently inconsistent explanation of prevalence and concentration remains a big challenge. Thus, this meta-analysis was conducted to determine the prevalence and concentration of harmful chemicals in breast milk in an African context. The databases MEDLINE, PubMed, Embase, SCOPUS, Web of Science, and Google Scholar were searched for both published and unpublished research. To conduct the analysis, the collected data were exported to Stata version 18. The results were shown using a forest plot and a prevalence with a 95% confidence interval (CI) using the random-effects model. The Cochrane chi-square (I2) statistics were used to measure the studies' heterogeneity, and Egger's intercept was used to measure publication bias. This review included twenty-eight studies with 4016 breast milk samples and newborns. The analysis showed the overall prevalence and concentration of aflatoxin M1 in breast milk were 53% (95% CI 40, 65; i2 = 98.26%; P = 0.001). The pooled mean aflatoxin M1 concentration in breast milk was 93.02 ng/l. According to this study, the eastern region of Africa was 62% (95% CI 39–82) profoundly affected as compared to other regions of the continent. In subgroup analysis by publication year, the highest level of exposure to aflatoxins (68%; 95% CI 47–85) was observed among studies published from 2010 to 2019. This finding confirmed that more than half of lactating women’s breast milk was contaminated with aflatoxin M1 in Africa. The pooled mean aflatoxin M1 concentration in breast milk was 93.02 ng/l. According to this study, the eastern region of Africa was profoundly affected compared with other regions. Thus, the government and all stakeholders must instigate policies that mitigate the toxicity of aflatoxins in lactating women, fetuses, and newborns.