Anemia remains a significant public health concern, particularly in developing countries like Sudan, where children are particularly vulnerable to its associated health implications. This study aimed to systematically assess the prevalence of anemia among Sudanese children. We conducted a comprehensive literature search in August 2021 and updated it in December 2022 to identify studies on anemia among Sudanese children. We searched databases including PubMed, Scopus, Science Direct, and Google Scholar. Studies eligible for inclusion in this systematic review and meta-analysis (SRMA) reported data to calculate anemia prevalence in children using WHO criteria. We performed meta-analysis using R software with metaprop and metafor packages. Using a random effects model, we estimated the pooled prevalence of anemia among 8006 Sudanese children to be 53.5% (95% CI, 36.6–70.4%). Subgroup analysis revealed that 62.7% of the children had unclassified anemia, 39.1% had iron deficiency anemia, and 8.7% had sickle cell anemia. Over a 21-year period, childhood anemia in Sudan showed an increasing trend, rising from 40.7% (1999–2009) to 55.1% (2010–2015) and 58.1% (2016–2020). The findings indicate a significantly higher prevalence of anemia among Sudanese children compared to many other countries, highlighting the need for proactive measures to prevent and control anemia in this population.