Background: The purpose of the study was to determine the effects of a social-ecologic intervention on health-related fitness (HRF) knowledge and behaviors of students (n = 62) living in rural areas. Methods: A prepost test control group design was constructed. In addition, qualitative data were collected by focus group discussions in the experimental group. Physical activity environment of a middle school was changed based on the social-ecologic model (SEM) with a focus on intrapersonal, interpersonal, community level, organizational factors, and public policies related to physical activity behavior. Health related fitness knowledge (HRFK) test, pedometer, and perceived physical activity self-efficacy and social support questionnaires were used for data collection. Results: Experimental group had significant improvement in HRF knowledge scores, physical activity levels, and social support compared with the control school students. The focus group results also supported the quantitative findings by indicating a perceived increase in physical activity opportunities; knowledge sources; and support from others. Conclusions: This study underlines the importance and positive outcomes of SEM in improving HRF knowledge, physical activity level, and social support of students in rural middle school settings.