Background: Previous studies have shown that fundamental movement skills (FMS) and physical activity are related. Specifically, earlier studies have demonstrated that the ability to perform a variety of FMS increases the likelihood of children participating in a range of physical activities throughout their lives. To date, however, there have not been studies focused on the development of, or the relationship between, these variables through junior high school (that is, between the ages of 13 and 15). Such studies might provide important insights into the relationships between FMS and physical activity during adolescence, and suggest ways to design more effective physical education programmes for adolescents. Purpose: The main purposes of the study are: (1) to investigate the development of the students' self-reported physical activity and FMS from Grade 7 to Grade 9, (2) to analyse the associations among the students' FMS and self-reported physical activity through junior high school, (3) to analyse whether there are gender differences in research tasks one and/or two. Participants and setting: The participants in the study were 152 Finnish students, aged 13 and enrolled in Grade 7 at the commencement of the study. The sample included 66 girls and 86 boys who were drawn from three junior high schools in Middle Finland. Research design and data collection: Both the FMS tests and questionnaires pertaining to self-reported physical activity were completed annually during a 3 year period: in August (when the participants were in Grade 7), January (Grade 8), and in May (Grade 9). Data analysis: Repeated measures multivariate analysis of variances (MANOVAs) were used to analyse the interaction between gender and time (three measurement points) in FMS test sumscores and self-reported physical activity scores. The relationships between self-reported physical activity scores and fundamental movement skill sumscores through junior high school were analysed using Structural Equation Modelling (SEM) with LISREL 8.80 software. Findings: The MANOVA for self-reported physical activity demonstrated that both genders' physical activity decreased through junior high school. The MANOVA for the FMS revealed that the boys' FMS sumscore increased whereas the girls' skills decreased through junior high school. The SEM and squared multiple correlations revealed FMS in Grades 7 and 8 as well as physical activity in Grade 9 explained FMS in Grade 9. The portion of prediction was 69% for the girls and 55% for the boys. Additionally, physical activity measured in Grade 7 and FMS measured in Grade 9 explained physical activity in Grade 9. The portion of prediction was 12% for the girls and 29% for the boys. In the boys' group, three additional paths were found; FMS in Grade 7 explained physical activity in Grade 9, physical activity in Grade 7 explained FMS in Grade 8, and physical activity in Grade 7 explained physical activity in Grade 8. Conclusions: The study suggests that supporting and encouraging FMS and physical activity are co-related and when considering combined scores there is a greater likelihood of healthy lifelong outcomes. Therefore, the conclusion can be drawn that FMS curriculum in school-based PE is a plausible way to ensure good lifelong outcomes. Earlier studies support that school physical education plays an important role in developing students FMS and is in a position to thwart the typical decline of physical activity in adolescence. These concepts are particularly important for adolescent girls as this group reflects the greatest decline in physical activity during the adolescent period.