Systemic lupus erythematosus (SLE) is a multisystem autoimmune disease with a suggested genetic basis. The newly identified human programmed cell death 1 gene could be associated with SLE susceptibility. We aimed to investigate the association between programmed cell death 1 polymorphism (PD1.3G/A (rs11568821) and PD1.5C/T (rs2227981)) with the risk of SLE in the Egyptian female population. This retrospective case–control study included 150 Egyptian females; 70 patients diagnosed to have SLE and 80 age-matched healthy controls. The two single nucleotide polymorphisms of the pdcd1 gene were genotyped by allelic discrimination through TaqMan real-time polymerase chain reaction. The PD1.3GG genotype and G allele as well as the PD1.5CC genotype were significantly more frequent in SLE patients (67.1%; p = 0.023, 82.1%; p = 0.0021, 62.9%; p = 0.0287 respectively). The GC haplotype was the most common haplotype among SLE patients (70.77%) with a reported significant linkage disequilibrium between the two studied polymorphisms ( p = 0.0041). Although most of the studies showed significant association of SLE with the minor alleles, we reported a significant association between the dominant genotypes (PD1.3GG and PD1.5CC) as well as the major G allele with the risk of SLE among Egyptian females.