The prevalence of overweight and obesity rates are rising throughout Asia, with Malaysia being at the forefront for the past years. The lack of recent data on young people, particularly university students in Malaysia has resulted in this study which sought to examine on the prevalence of overweight and obesity among university students and effect of physical activity brain breaks at one public university in Sarawak, Malaysia. The health-related fitness test (HRFT) was administered while physical activity brain breaks (PABB) videos were used as an intervention tool. Descriptive analysis and paired sample t-test were used. For the Body Mass Index (BMI), results revealed that the frequency of participants increased significantly from pre (52.1%) to post (75.0%) in the normal weight category. Besides, the frequency of the participants decreased from pre-to -post in the underweight (2.1–0.0%), overweight (20.8–14.6%) and obese (25.0–10.4%) category. In terms of HRFT test, the frequency of participants increased from pre to post in superior fitness level (18.8–52.1%) and excellent fitness level (12.5–20.8%). Conversely, the participants’ frequency declined from pre to post in the fit fitness level (31.2–16.7%), poor fitness level (37.5–10.4%). Moreover, paired sample t-test on HRFT test revealed that there was significant increase from pre to post test in step test, p = .002, curl-ups, p = .004, and sit and reach, p = .005. Additionally, the paired sample t-test for HRFT test for pre and post-test based on groups showed statistically significant increase on the intervention group, whereby there was significant increase from pre to post on step test, p = .001, push-ups, p = .004, curl-ups, p = .011, and sit and reach, p = .001. The study revealed important findings that can be applied to devise strategic interventions at improving the health and fitness of the university students.