BackgroundOver 80,000 pregnant women died in Nigeria due to pregnancy-related complications in 2020. Evidence shows that if appropriately conducted, caesarean section (CS) reduces the odds of maternal death. In 2015, the World Health Organization (WHO), in a statement, proposed an optimal national prevalence of CS and recommended the use of Robson classification for classifying and determining intra-facility CS rates. We conducted this systematic review and meta-analysis to synthesise evidence on prevalence, indications, and complications of intra-facility CS in Nigeria.MethodsFour databases (African Journals Online, Directory of Open Access Journals, EBSCOhost, and PubMed) were systematically searched for relevant articles published from 2000 to 2022. Articles were screened following the PRISMA guidelines, and those meeting the study’s inclusion criteria were retained for review. Quality assessment of included studies was conducted using a modified Joanna Briggs Institute’s Critical Appraisal Checklist. Narrative synthesis of CS prevalence, indications, and complications as well as a meta-analysis of CS prevalence using R were conducted.ResultsWe retrieved 45 articles, with most (33 (64.4%)) being assessed as high quality. The overall prevalence of CS in facilities across Nigeria was 17.6%. We identified a higher prevalence of emergency CS (75.9%) compared to elective CS (24.3%). We also identified a significantly higher CS prevalence in facilities in the south (25.5%) compared to the north (10.6%). Furthermore, we observed a 10.7% increase in intra-facility CS prevalence following the implementation of the WHO statement. However, none of the studies adopted the Robson classification of CS to determine intra-facility CS rates. In addition, neither hierarchy of care (tertiary or secondary) nor type of facility (public or private) significantly influenced intra-facility CS prevalence. The commonest indications for a CS were previous scar/CS (3.5–33.5%) and pregnancy-related hypertensive disorders (5.5–30.0%), while anaemia (6.4–57.1%) was the most reported complication.ConclusionThere are disparities in the prevalence, indications, and complications of CS in facilities across the geopolitical zones of Nigeria, suggestive of concurrent overuse and underuse. There is a need for comprehensive solutions to optimise CS provision tailor-made for zones in Nigeria. Furthermore, future research needs to adopt current guidelines to improve comparison of CS rates.Supplementary InformationThe online version contains supplementary material available at 10.1186/s12978-023-01598-9.