(1) Background: It has been identified that schools that adopt at least two hours a week of physical education and plan specific contents and activities can achieve development goals related to physical level, such as promoting health, well-being, and healthy lifestyles, on a personal level, including bodily awareness and confidence in physical skills, as well as a general sense of well-being, greater security and self-esteem, sense of responsibility, patience, courage, and mental balance. The purpose of this study was to establish the effect of physical education programs on the physical activity and emotional well-being of primary school children. (2) Methods: The experimental group comprised 45 girls and 44 boys aged 6–7 years (First Grade) and 48 girls and 46 boys aged 8–9 years (Second Grade), while the control group comprised 43 girls and 46 boys aged 6–7 years (First Grade) and 47 girls and 45 boys aged 8–9 years (Second Grade). All children attended the same school. The Children’s Physical Activity Questionnaire was used, which is based on the Children’s Leisure Activities Study Survey questionnaire, which includes activities specific to young children (e.g., “playing in a playhouse”). Emotional well-being status was explored by estimating three main dimensions: somatic anxiety, personality anxiety, and social anxiety. The Revised Children’s Manifest Anxiety Scale (RCMAS) was used. (3) Results: When analysing the pre-test results of physical activity of the 6–7- and 8–9-year-old children, it turned out that both the First Grade (92.15 MET, min/week) and Second Grade (97.50 MET, min/week) participants in the experimental group were physically active during physical education lessons. When exploring the results of somatic anxiety in EG (4.95 ± 1.10 points), both before and after the experiment, we established that somatic anxiety in EG was 4.55 ± 1.00 points after the intervention program, demonstrating lower levels of depression, seclusion, somatic complaints, aggression, and delinquent behaviours (F = 4.785, p < 0.05, P = 0.540). (4) Conclusions: We established that the properly constructed and purposefully applied eight-month physical education program had positive effects on the physical activity and emotional well-being of primary school children (6–7 and 8–9 years) in three main dimensions: somatic anxiety, personality anxiety, and social anxiety. Our findings suggest that the eight-month physical education program intervention was effective at increasing levels of physical activity. Changes in these activities may require more intensive behavioural interventions with children or upstream interventions at the family and societal levels, as well as at the school environment level. These findings have relevance for researchers, policy makers, public health practitioners, and doctors who are involved in health promotion, policy making, and commissioning services.