BackgroundDespite substantial improvements in accessibility of Anti-Retroviral Treatment (ART), death of children on ART remains a prevailing challenge in sub-Saharan African (SSA) countries. However, the pooled magnitude of mortality at different ART follow-up periods remains unknown for the region. We estimated the pooled proportion of all-cause mortality for pediatric patients receiving first-line ART at 3, 6, 12, and 24 months follow-up period in SSA.MethodsWe searched for relevant articles published between January 2014 and June 2018 on PubMed, Hinari and Google scholar databases. We searched for additional articles from reference lists and 2014–2018 abstracts archived by the Conference on Retroviruses and Opportunistic Infections (CROI) and the International AIDS Society Conference on HIV Science (IAS).ResultsWe reviewed 29 articles reporting mortality among pediatric ART patients at different follow-up periods in countries from 2001 to 2016. Among the 51,619 pediatric ART patients in these cohorts, studies reported 4061 (7.9%) all-cause cumulative death. The cumulative pooled proportion of mortality at 3, 6, 12 and 24 months of ART were 3% (95% CI: 3.0–4.0), 5% (95% CI: 4.0–6.0), 6% (95% CI: 5.0–7.0) and 7% (95% CI: 6.0–8.0), respectively.ConclusionsIn SSA, significant proportion of mortality among children occurs in the first 3–6 months of ART initiation. Western Africa has a little higher estimate of mortality among pediatric ART patients at 6 and 12 months of follow-up. Strategies to prevent early mortality including thorough screening and management of opportunistic infections before ART initiation are needed.Electronic supplementary materialThe online version of this article (10.1186/s12889-019-6482-1) contains supplementary material, which is available to authorized users.