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Thrombotic complications, particularly stroke, are significant causes of morbidity in children with sickle cell disease (SCD). While the Factor V Leiden (FVL) G1691A mutation is a recognized genetic risk factor for thrombophilia in Caucasian and Middle Eastern populations, its role in African pediatric SCD patients remains unclear. To determine the prevalence of the FVL G1691A mutation and its association with activated protein C resistance in Sudanese pediatric SCD patients with a history of cerebrovascular accidents. This descriptive cross-sectional study was conducted from December 2015 to May 2016 at Jaafar Ibn Auf Specialized Hospital for Children in Khartoum, Sudan. One hundred Sudanese children (<18 years) with homozygous SCD and documented cerebrovascular accidents were recruited. Genotyping for FVL was performed using allele-specific polymerase chain reaction (PCR), and activated protein C resistance was assessed using a clotting-based assay. Demographic, clinical, and familial data, including tribal affiliation and parental consanguinity, were collected. Data were analyzed using SPSS V29. Among the 100 participants (mean age 6.1 ± 3.3 years; 57% male), 2% were heterozygous for the FVL mutation (GA genotype), and none were homozygous mutants. Both heterozygous individuals demonstrated resistance to activated protein C. Parental consanguinity was reported in 79% of cases. No other FVL-associated thrombophilia was detected in the remaining 98 patients, all of whom had the wild-type genotype. The FVL mutation is rare among Sudanese pediatric SCD patients with stroke, suggesting it is unlikely to be a significant contributor to thrombosis risk in this population. These findings support the need for broader genetic and clinical investigations to identify more relevant risk factors and inform stroke prevention strategies in African children with SCD.