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Malaria remains a substantial global health challenge, causing preventable illnesses and fatalities. In Nepal, the government has ambitiously targeted achieving malaria-free status by 2025. This study aims to assess the impact of women’s roles on health-seeking behavior during suspected malaria fever in the high-risk area of Kanchanpur district, Nepal. This is a cross-sectional analytical design with a mixed-method approach, the research focused on Kanchanpur district, selected from 20 high-risk malaria districts of Nepal. Belauri Municipality within Kanchanpur, identified for its concentration of high and moderate-risk wards, was the specific study area. A random selection process identified 387 households for a comprehensive survey. Face-to-face interviews with household heads were conducted after obtaining written informed consent and ethical approval from the Nepal Health Research Council (March 3, 2023/Ref no.-2041). Data analysis, employing statistical measures such as percentages, frequency, mean, and the Chi-square test, was performed using SPSS version 20. Cultural beliefs regarding women’s use of bed nets during menstruation significantly predicted health-seeking behavior (p-value < 0.05). Those endorsing bed net use during menstruation were nearly twice as likely to choose modern health facilities (COR = 1.975, 95% C.I. = 1.134 to 3.439, p = 0.016). Women’s involvement in malaria treatment decisions strongly correlated with health-seeking behavior (p-value = 0.001). However, women participating in household decisions for suspected malaria treatment were less likely to choose modern health facilities (COR = 0.327, 95% CI = 0.171–0.627, p = 0.001) compared to those without such a role. The study underscores the complex influence of cultural beliefs and women’s decision-making roles on health-seeking behavior. Recognizing and comprehending these factors are vital for crafting effective malaria interventions that align with cultural contexts and consider the nuanced roles of women in health-related decisions.