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Objective: The burden of extra‐pulmonary tuberculosis (EPTB) is not well quantified in TB endemic countries such as those in sub‐Saharan Africa. This study aimed to quantify that burden via a systematic review of the prevalence of EPTB in African countries. Methods: Studies were retrieved by searching five databases; 105 studies published between 1990 and 2023 were included. The studies described the prevalence of EPTB among the general population (4 studies), TB patients (68) and patients with other conditions, including HIV (15), meningitis (3), renal failure (3) and other comorbidities, some of which are cancer (12). Due to the low number of studies reporting EPTB in patients with conditions other than TB, the meta‐analysis was performed on studies reporting on EPTB among TB patients (68 studies). Meta‐analysis was performed on the 68 studies (271,073 participants) using a random‐effects model to estimate the pooled prevalence of EPTB. Meta‐regression was used to explore possible explanations for heterogeneity according to regions and time periods. Results: The pooled prevalence of EPTB among TB patients was 26% (95% CI 23–29%). There was substantial heterogeneity of prevalence for the five African regions. The Eastern region had the highest prevalence of 32% (95% CI 28–37%) and the lowest in Western Africa, 16% (95% CI 10–24%). There was no significant difference in the prevalence of EPTB between the 3 eleven‐year time periods. Conclusions: Our systematic review and meta‐analysis give insight into the burden of EPTB in Africa. This review could inform clinical and programmatic practices–a higher suspicion index for clinicians and more effort for better services. This could contribute to efforts aiming to end TB, which have historically been focused on PTB.Coordinated efforts that target both EPTB and PTB are needed. [ABSTRACT FROM AUTHOR]