Pacific Island countries experience a high prevalence of noncommunicable diseases (NCDs), which may be prevented by reducing risk behaviors and strengthening protective factors in childhood and adolescence. To better inform preventative interventions, our objective was to use publicly available data from the Global School-based Student Health Survey (GSHS), to provide cross-sectional and trend estimates for the prevalence of NCD risk and protective factors among school-aged children in 2011 and 2017 in Samoa. Two waves of cross-sectional data included 4,373 children (51.98% female), with a median age of 15 years, who were mainly in school years 9–10 in Samoa. Retrospective analyses were adjusted for the GSHS multistage stratified cluster sample design. Weighted prevalences of overweight/obesity, dietary behaviors, physical activity, and sedentary behavior, oral and hand hygiene, emotional and mental health, and community protective factors were reported by study year. Logistic regressions were fitted to assess differences in the prevalence of risk and protective factors, adjusted for age group, sex, and school year. In 2011 and 2017, the prevalence of overweight/obesity remained consistently high in females (59.12% and 64.29%, p = 0.428) and increased from 44.21% to 53.65% in males (p = 0.039). Time spent sitting for long periods, smoking cigarettes, using other tobacco products, and drinking alcohol were lower in 2017 compared to 2011 (all p<0.05). Many children reported experiencing bullying (33.27% for females and 59.30% for males in 2017), while physical fighting was common among males (73.72% in 2011 and 57.28% in 2017). The high prevalence of obesity and related NCD risk factors require urgent public health action in Samoa. Alongside the continued reduction of tobacco and alcohol use, emotional and mental wellness should be prioritized in interventions and programs to promote healthy behaviors and lifestyle changes starting in childhood.