BackgroundInternalisation of stigma occurs when people with a stigmatised attribute, such as a mental illness, supress negative but accepted societal attitudes. However, as far as is known, there is no comprehensive picture of the prevalence of and factors associated with, internalised stigma among people living with mental illness in Africa. This systematic review and meta-analysis provide new knowledge by examining the evidence on the prevalence of internalised stigma and associated factors among people living with mental illness in Africa.MethodsUsing the population, intervention, comparison, outcome, and type of study (PICOT) approach, PubMed, Scopus, MEDLINE, PsycINFO, CINAHL, ScienceDirect, and Google Scholar were searched using a structured search comprising terms associated with mental health, mental illness, internalised stigma, and a list of all African countries. To evaluate paper quality, the Joanna Briggs Institute Quality Appraisal Checklist was used. Subgroup analysis with country and diagnosis was tested using a random-effect model, and bias was checked using a funnel plot and an inspection of Egger’s regression test. A p-value, OR and 95% CI was used to demonstrate an association.ResultsThe pooled prevalence of internalised stigma was 29.05% (25.42,32.68: I2= 59.0%, p ≤ 0.001). In the subgroup analysis by country, Ethiopia had the highest prevalence of internalised stigma at 31.80(27.76,35.84: I2= 25.6%, p ≤ 0.208), followed by Egypt at 31.26(13.15,49.36: I2= 81.6%, p ≤ 0.02), and Nigeria at 24.31(17.94,30.67: I2= 62.8%, p ≤ 0.02). Based on domains of internalised stigma, pooled prevalence was stigma resistance: 37.07%, alienation: 35.85%, experience of discrimination: 31.61%, social withdrawal: 30.81% and stereotype: 26.10%. Experiencing psychotic symptoms (1.42(0.45,2.38)), single marital status (2.78(1.49,4.06)), suicidal ideation (2.32(1.14,3.49)), drug nonadherence (1.5(-0.84,4.00)), poor social support (6.69(3.53,9.85)), being unemployed (2.68(1.71,3.65)), and being unable to read and write (3.56(2.26,4.85)) were identified as risk factors for internalised stigma.ConclusionsInternalised stigma is common among people suffering from mental illnesses in Africa. This review determined that 29% of the sample population had elevated internalised stigma scores, and there were variations by country. People experiencing mental illness who have a single marital status, suicidal behaviours, poor social support, unemployed and have poor literacy levels were at a higher risk of internalised stigma. The finding points to populations that require support to address internalised stigma and improve the mental health outcomes.Supplementary InformationThe online version contains supplementary material available at 10.1186/s12888-023-04950-2.