Background Tuberculous meningitis is a serious public health problem, particularly in low-income countries. It is associated with high rates of mortality and morbidity. The outcome of tuberculous meningitis in children is not well documented in Ethiopia, particularly in eastern Ethiopia. This study aimed to determine the treatment outcomes of tuberculous meningitis at discharge and its associated factors in eastern Ethiopia. Methods An institutional-based retrospective cross-sectional study was conducted on 121 children who were admitted and treated for tuberculous meningitis between January 2017 and December 2021. Data were collected using a pretested checklist, coded and entered into EpiData version 3.1, and analyzed using Statistical Package for the Social Sciences (SPSS) version 25. Factors associated with treatment outcomes were identified using multivariable logistic regression analyses. The association was described using the adjusted odds ratio (AOR) at a 95% confidence interval (CI). Finally, statistical significance was set at a p-value <0.05. Results Of the 121 medical records of children, 33.9% (95% CI:25–42%) died. Among the survivors, 28.1% were discharged with neurological sequelae and the remains (38.0%) were discharged with normal outcomes. In multivariable analyses, nutritional status (AOR=2.87; 95% CI:1.04–7.94), duration of illness (AOR = 0.33; 95% CI: 0.15–0.86), hydrocephalus (AOR=3.78; 95% CI:1.08–13.34), and stage-III Tuberculous Meningitis (AOR = 5.29; 95% CI:1.88–14.84) were identified as significantly associated factors with poor clinical outcomes. Conclusion The treatment outcomes for tuberculous meningitis in children are unfavorable. Two-thirds of children had poor treatment outcomes. Malnutrition, disease stage, hydrocephalus, and illness duration were associated with poor treatment outcomes at discharge. Health workers in primary health care should be aware of the importance of early screening, diagnosis, and treatment to improve clinical outcomes and reduce associated mortality and disability. In practice, more attention should be paid to children with malnutrition and hydrocephalus.