Physical activity (PA) could be protective against hypertension, atherosclerosis, coronary heart disease and cardiovascular disease. This quantitative study assessed the association between a PA intervention and three anthropometric parameters (weight, body mass index, body fat) and four physiological parameters (cholesterol level, systolic blood pressure, diastolic blood pressure, heart rate) among secondary school pupils (N = 160) in Egypt through the school term. The pupils were randomised to an intervention group (80 pupils) and controls (80 pupils). Measurements were obtained for all pupils twice: at baseline; and then again after three months. The PA intervention programme comprised an ‘afterschool’ one hour of moderate exercise three times a week for three months. Both the controls and the intervention pupils attended the ‘normal’ exercise schedule provided by the school; in addition, the intervention group attended afterschool PA programme from about 2–3 o’clock in the afternoon. At baseline, employing pupil’s BMI, 27.5% and 28.8% of the intervention and control pupils respectively were classified as overweight. After three months, the percentage of overweight decreased to 12.5% in the intervention pupils, while it increased to 37.3% in the controls. At the end of the three months period, there were significant improvements across most anthropometric and physiological parameters of the intervention pupils when compared with the control children. The correlation coefficient of the improvements for the boys and the girls was 0.97, indicating clearly that the intervention was having nearly the same beneficial effect for boys and girls. A moderate PA programme for a modest period of 3 months could be effective in maintaining or enhancing pupil’s anthropometric and physiological parameters in comparison to the controls where there was deterioration in both parameters. Policy makers and secondary schools in Egypt might need to pay more attention to PA programmes conducted on school days, in order to motivate pupils to attend such programmes. There is also an urgent need to look at current PA systems within schools in Egypt in order to assess PA outside school times.