Background In low-income nations, high-risk fertility behavior is a prevalent public health concern that can be ascribed to unmet family planning needs, child marriage, and a weak health system. As a result, this study aimed to determine the factors that influence high-risk fertility behavior and its impact on child stunting and anemia. Method This study relied on secondary data sources from recent demography and health surveys of nine east African countries. Relevant data were extracted from Kids Record (KR) files and appended for the final analysis; 31,873 mother-child pairs were included in the final analysis. The mixed-effect logistic regression model (fixed and random effects) was used to describe the determinants of high-risk fertility behavior (HRFB) and its correlation with child stunting and anemia. Result According to the pooled study about 57.6% (95% CI: 57.7 to 58.2) of women had at least one high-risk fertility behavior, with major disparities found across countries and women’s residences. Women who lived in rural areas, had healthcare access challenges, had a history of abortion, lived in better socio-economic conditions, and had antenatal care follow-up were more likely to engage in high-risk fertility practices. Consequently, Young maternal age at first birth (<18), narrow birth intervals, and high birth orders were HRFBs associated with an increased occurrences of child stunting and anemia. Conclusion This study revealed that the magnitude of high-risk fertility behavior was higher in east Africa region. The finding of this study underscores that interventions focused on health education and behavioral change of women, and improvement of maternal healthcare access would be helpful to avert risky fertility behaviors. In brief, encouraging contraceptive utilization and creating awareness about birth spacing among reproductive-age women would be more helpful. Meanwhile, frequent nutritional screening and early intervention of children born from women who had high-risk fertility characteristics are mandatory to reduce the burden of chronic malnutrition.