Background: Despite the high prevalence of podoconiosis and its impact on affected individuals, there was a paucity of research exploring the factors associated with stigma among podoconiosis patients in Rwanda. Stigmatization exacerbates the already considerable challenges faced by individuals afflicted with this condition, impeding their access to healthcare, social support, and economic opportunities. The main objective of this study was to assess the factors contributing to stigma among podoconiosis patients attending Heart and Sole Africa treatment center located in Musanze District of Northern Rwanda. Methodology: The quantitative cross-sectional study design employed included 183 participants who were selected among 500 podoconiosis patients using the Cochrane formula for sample size calculation and a systematic random sampling method was used. A pretested questionnaire was used to collect data. Data analysis was conducted using SPSS version 26. Pearson chi-square test was carried out and a P-value less than 0.05 was considered as statistically significant. The enter method was used to control confounding variables in a binary logistic regression analysis. Results: Out of the 183 participants, 83% (151 individuals) had a stigma related to podoconiosis. the factors associated with stigma were; sex, marital status, education level, household income, residence, severity of disease, being currently following treatment, and the clinical stage of podoconiosis. Females had a significantly lower odds of the outcome compared to males (AOR) of 0.12 (65% CI: 0.23-0.04, p=0.007).), participants earning below 50,000Frw per month were much more likely to experience stigma (AOR of 5.18, 65% CI: 3.07-8.46, p < 0.001), urban participants had significantly higher odds of facing stigma compared to those in rural areas (AOR of 6.82, 65% CI: 3.12-14.57, p = 0.048) and the patients in stage 3 or higher had much greater odds of experiencing stigma (AOR of 5.12, 65% CI: 2.06-8.18, p = 0.001). Conclusion: Results indicate a high stigma among podoconiosis patients and therefore it is recommended that policies and interventions regarding podoconiosis management in Rwanda must be developed by different policymakers and stakeholders.