Menstrual discrimination hampers progress toward Sustainable Development Goals. Examining the spatial heterogeneity of menstrual discriminatory practices may present an opportunity for targeted interventions. Here we evaluate geographical disparities in menstrual-related restrictions and assess their association with socio-economic and demographic factors. We used data from the 2022 Nepal Demographic and Health Survey which included 13,065 women aged 15–49 who reported menstruating within the past year. We explored the spatial heterogeneity of menstrual restriction outcomes using the standard Gaussian kernel density approximation method and the spatial scan statistic. The Poisson regression model with robust standard errors was used to assess the association between the different forms of menstrual restriction and the socio-economic, and demographic factors. Overall, the prevalence of women who reported any form of menstrual restriction was 84.8% and was subject to geographical variations ranging from 79.0% in Bagmati to 95.6% in Sudurpashchim. Religious restrictions were the most prevalent (79.8%) followed by household-level restrictions (39.5%) and then Chhaupadi (6.2%). Geographical variations were more prominent for women experiencing Chhaupadi (primary geographical cluster: relative risk = 7.4, p<0.001). Strikingly, women who reside in households led by female household heads were less likely to report experiencing household-level restriction during menstruation (Adjusted prevalence ratio (aPR) = 0.89, [95%CI: 0.84–0.94], p<0.001) whilst those residing in wealthy households were less likely to report experiencing Chhaupadi (aPR = 0.26, [95%CI: 0.17–0.39], p<0.001; among the richest). Our study demonstrated marked geographical micro-variations in menstrual discriminatory practices in Nepal. Policymakers should implement preventive behavioral interventions in the most vulnerable geographic areas to effectively and efficiently reduce the overall prevalence of menstrual discrimination. It is crucial to prioritize the designing and testing of targeted interventions to determine their effectiveness against Chhaupadi in these high-prevalence settings. Additionally, empowering women appears to be a promising strategy for combating menstrual discrimination within the household.