Purpose <p>Gender-based differences have been shown to affect the prognosis of various tumors, but their role in the survival of rectal neuroendocrine tumors (RNETs) remains unclear. Therefore, we aimed to explore the gender-based differences in the prognosis of RNETs using the Surveillance, Epidemiology, and End Results (SEER) database.</p> Materials and methods <p>RNETs patients from 2000 to 2020 were identified from the SEER database. Propensity score matching (PSM) was used to minimize selection bias. Kaplan–Meier analyses and Cox proportional hazard models were applied to evaluate the impact of clinical characteristics on overall survival (OS) and cancer-specific survival (CSS).</p> Results <p>A total of 8247 patients were analyzed, comprising 3990 males and 4257 females. Among the male patients, there was a notably higher proportion of Caucasians and cases of distant metastasis. Before PSM, male patients displayed significantly poorer OS (<i>P</i> &lt; 0.001) and CSS (<i>P</i> &lt; 0.001) compared to female patients. Additionally, they exhibited lower mean OS and CSS rates at 3-, 5-, and 10-year intervals (<i>P</i> &lt; 0.05). After PSM, male patients continued to demonstrate inferior OS (<i>P</i> &lt; 0.001) and CSS (<i>P</i> = 0.031) compared to female patients. Similarly, they maintained lower mean OS and CSS rates across the 3-, 5-, and 10-year intervals (<i>P</i> &lt; 0.05). Multivariate Cox regression identified marital status, age, race, gender, NM stage, surgery, chemotherapy, and tumor size as independent risk factors for OS; marital status, age, gender, TNM stage, surgery, and tumor size for CSS.</p> Conclusions <p>Male RNET patients exhibit significantly poorer OS and CSS than females, independent of clinical covariates. Gender emerges as a critical prognostic factor in RNETs. Future studies should explore biological mechanisms underlying gender disparities and validate these findings in prospective cohorts to inform gender-stratified clinical decision-making.</p>