Background <p>Malaria is a major public health problem in Sub-Saharan Africa (SSA), causing a considerable burden on households and health systems. This systematic review analyses the malaria treatment cost faced by households and health systems in Sub-Saharan Africa (SSA).</p> Methods <p>The review was conducted according to the Preferred Reporting Items for Systematic Reviews (PRISMA) guideline. Studies reported malaria treatment costs incurred by households and the health system in SSA were included in the review. A pooled estimate for household and health system costs of malaria was conducted using the random effects model of the Residual Maximum Likelihood (REML) method. The analysis is conducted in STATA version 16. A total of 39 studies were included in the review, of which approximately 56% reported household costs and 23% reported health system costs.</p> Results <p>The pooled estimated household cost per outpatient malaria episode was $12.55 (95% CI $9.58, $16.45, <i>I</i>² = 96.29%, P &lt; 0.01), while the pooled inpatient cost per severe malaria episode was $53.71 (95% CI $41.00, $70.31, <i>I</i>² = 96.22%, P &lt; 0.01). Households in the poorest quintile incurred the highest malaria treatment costs compared with those in the richest quintile. The pooled estimated health system cost per outpatient malaria episode was $19.91 (95% CI $10.77, $36.81, <i>I</i>^<i>2</i> = 92.44%, P &lt; 0.01), while the health system inpatient cost per severe malaria was $64.03 (95% CI $48.86, $83.90,<i> I</i>^<i>2</i> = 93.01%, P &lt; 0.01).</p> Conclusions <p>Malaria imposed a substantial economic burden on health system and households in low-income countries in SSA. Our findings provide evidence to guide malaria programs planning and enhance resource allocation in SSA.</p> <p><i>PROSPERO registration number</i>:&#xa0;CRD420251266073.</p>