Many school-based physical activity (PA) interventions have been developed, but only a few have assessed their long-term effects. A PA intervention taking place in the first four years of some Slovenian primary schools entails an enhanced physical education (PE) curriculum, including two extra lessons of PE per week, a wider selection of PE content, and additional outdoor education delivered by both a specialist PE teacher and a general teacher. The effects of the intervention on children's physical fitness (motor tasks and anthropometry) were evaluated within a quasi-experimental study. In total, 324 children from nine Slovenian primary schools either received the enhanced curriculum (intervention (n=160)) or standard PE (control (n=164)), and were followed for a four-year intervention period and seven years post intervention. Data from the SLOFIT database were used to compare differences in the physical fitness of children each year. Linear Mixed Models were used to test the influence of the PA intervention. Over an 11-year period, the PA intervention group significantly differed in all motor tasks, but not in anthropometric measures or body mass index, after controlling for year of measurement and sex. Differences between the control and intervention groups decreased with time. This study highlights the importance of tracking the long term effects of PA interventions. PA intervention in the first four years of Slovenian primary school offers the possibility of improving physical performance in children; initiatives aiming to increase their performance (physical fitness, physical activity) and health outcomes are warranted.