The purpose of our meta-analysis is to examine the associations between three single nucleotide polymorphisms of endothelial nitric oxide synthase (eNOS) gene, G894T, intron 4 and T-786C, and the risk of erectile dysfunction. An electronic database search was performed to identify case-control studies reporting the association between single nucleotide polymorphisms of eNOS gene and erectile dysfunction. Stringent inclusion and exclusion criteria were employed to select high-quality studies for this meta-analysis. Comprehensive Meta-analysis 2.0 software (Biostat Inc., Englewood, New Jersey, USA) was used for statistical analysis of the data extracted from the selected studies. From the initial 203 articles retrieved from database search, this meta-analysis finally selected 12 high-quality case-control studies that conformed to our inclusion criteria. The 12 studies contained a total of 1962 patients with erectile dysfunction and 1752 healthy controls. The results of our meta-analysis showed that G894T correlated with an increased risk erectile dysfunction under both the allele and dominant models (allele: OR = 1.556, 95% CI = 1.064–2.275, P = 0.023; dominant: OR = 1.613, 95% CI = 1.050–2.476, P = 0.029). A similar association was found between T-786C and erectile dysfunction under the allele model (OR = 1.679, 95% CI = 1.341–2.102, P < 0.001), but not under the dominant model (all P > 0.05). Our meta-analysis showed that the two single nucleotide polymorphisms in eNOS gene, G894T and T-786C, are strongly associated with the risk of erectile dysfunction.