Background: The absence of Physical Education (PE) from the South African school curriculum before its reintroduction in recent years contributed to health concerns regarding the low physical activity (PA) levels of children and adolescents in South Africa. Purpose: This study evaluated the effects of a once-a-week enhanced quality PE programme on the PA levels of South African Grade 7 learners. Methods: Using a pre-test and post-test control-group design, 110 Grade 7 learners aged 12-13 years (experimental school, n = 40; control schools, n = 70) from two primary schools in Potchefstroom, South Africa, were studied. They participated in a 12-week PE intervention programme based on the guidelines of the South African Curriculum and Assessment Policy Statement, which allocates one hour per week to PE teaching. The intervention included five quality-enhancing components, namely well-trained teachers, homework activities, a reward system, hand-made apparatus and the monitoring of activity intensity. In the experimental school, 40 learners were randomly assigned from the total Grade 7 class (n = 124) to the experimental group, while two control groups (n = 37 and n = 33) were used, one from the same school as the experimental school and the other from a different school. Additionally, to control for PE teacher interaction effect, the experimental group was divided into 4 experimental sub-groups of 10 learners each, which were taught by 4 different PE teachers, and the pre-test and post-test data of these experimental sub-groups were also analysed. Children's PA levels were measured before and after the intervention using a validated Children's Leisure Activities Study Survey questionnaire. The Kruskal-Wallis and Wilcoxon signed-rank tests were used to evaluate the effects of the intervention programme. Results: No significant differences were found within the experimental group between the 4 experimental sub-groups and between the 2 control groups at pre- and post-test measurements (p > 0.05). There was a significant effect for the experimental group as a whole, as results of the total experimental group showed statistically significant increases in moderate PA (ES = 0.47; p = 0.014), vigorous PA (ES = 0.48; p = 0.012) and total PA (ES = 0.51; p = 0.008) as well as decreases in sedentary behaviours (ES = 0.39; p = 0.041) after the 12-week intervention programme, whereas no significant changes were found in the control group. Statistically significant improvements were also found in all 4 experimental sub-groups between pre- and post-tests for the time spent in moderate PA (p = 0.028-0.05; ES = 0.23-0.64), vigorous PA (p = 0.018-0.036; ES = 0.23-0.63), total PA (p = 0.017-0.05; ES = 0.30-0.68) and sedentary time (p = 0.014-0.049; ES = 0.26-0.66), whereas no marked changes were observed among the two control groups, indicating no PE teacher interaction effect on the results. Conclusions: The enhanced quality PE programme can be used as a valuable framework for PE implementation targeted at promoting learners' PA levels, even in the presence of restricted time allocation, and limited teaching and learning resources.