Intermittent monitoring of health risk behaviours at the population level is important for the planning and evaluation of national health promotion intervention programmes. The study aimed to provide trend estimates on the prevalence of various health risk behaviours assessed in the Global School-based Health Survey in 2003, 2007 and 2011 in the Philippines. Three waves of cross-sectional data included 18,285 school-going adolescents, 47.4% male and 52.6% female, aged between 11 years or younger and 16 years or older, with a mean age of about 14.7 years (SD = 1.2), and mainly in second to fourth year study Grade. Significant improvements in health risk and risk behaviours (overweight or obese and smokeless tobacco use among boys, being in a physical fight, troubles from alcohol drinking, mental health, oral and hand hygiene among both boys and girls) but also increases in health risk behaviour (bullying victimization, injury and loneliness) among both boys and girls were found in this large study over a period of eight years in the Philippines. High prevalences of health risk behaviours and increases in some of them should call for intensified school health promotion programmes to reduce such risk behaviours.