Background: Women, particularly those with young children, engage in less leisure-time physical activity (LTPA) than men. Additionally, mothers living in rural areas have more difficulty participating in LTPA than those in urban areas. The aim of this study was to analyze the challenges faced by mothers of rural areas of Gipuzkoa in LTPA participation, from a feminist perspective. Methods: A total of 129 mothers (age 41.5 ± 5.9; 45.7% inactive) with young children completed the Gipuzkoa Women’s Physical Activity Questionnaire. Concurrently, four focus groups were organized in four different municipalities, in which 19 mothers of young children participated (13 were inactive). Barriers were classified based on the socioecological perspective. Results: The most frequently mentioned intrapersonal barriers were lack of time due to work and caregiving, age-/pregnancy-/motherhood-related health issues, and a feeling of rejection toward LTPA. The most relevant interpersonal barriers were a lack of partners to do LTPA with and a lack of spouse support. The main environmental barriers were related to the shortage of facilities and activities suited to their needs and the rugged terrain. Conclusions: Mothers of young children living in rural areas face barriers twice over: because they are women and mothers and because they live in a rural environment. It therefore seems important to consider their perceived barriers to design, develop, and implement strategies to promote LTPA among this population group.