Several orofacial painful conditions are influenced by gender-related factors, but no studies are available with regard to Burning Mouth Syndrome (BMS). The present study aimed at investigating gender differences among BMS patients and their influence on pain perception. 242 BMS males (BMSm) and 242 BMS females (BMSf) matched for age were consecutively enrolled. Sociodemographic and clinical characteristics were recorded and the numeric rating scale (NRS), the Total Pain Rating Index (T-PRI), the Hamilton rating scale for anxiety and depression (HAM-A, HAM-D), the Pittsburgh sleep quality index (PSQI) and the Epworth sleepiness scale (ESS) were administered. The BMSm presented statistically significant higher levels of education and rate of employment compared to the BMSf (p-values: 0.001**). Moreover, the BMSm were greater consumers of alcohol and had a higher BMI than the BMSf (p-values: < 0.001**, 0.034*). With respect to systemic comorbidities, cardiovascular diseases were statistically more prevalent among the BMSm, while hypothyroidism was more frequent in the BMSf (p-vales: < 0.001**). No differences were noted between the two groups in terms of oral symptoms and in the median scores of NRS, T-PRI, HAM-A, HAM-D, PSQI and ESS. Interestingly, the multivariate regression analysis revealed that, while anxiety, high BMI, poor sleep and high level of T-PRI were correlated to the intensity of pain (NRS) in both groups, low education was additional predictor of pain in BMSf. Further, depression, alcohol and intensity of pain were factors positively associated to the quality of pain (T-PRI) in the BMSm, whereas low education, non-married status and NRS were correlated to the T-PRI, in the BMSf. Surprisingly, smoking was inversely correlated to the intensity of pain and quality of pain respectively in BMSf and BMSm. Sociodemographic and risk factors were found to differently influence pain perception in BMSm and BMSf. Therefore, clinicians should take into account gender differences in the assessment of BMS patients to better tailor the overall pain management.