Studies have shown the prevalence of mental health and obesity among adolescents is at increasing trend due to urbanisation and changes in lifestyle. This study is to investigate the level of stress and its impact on eating behaviour among Malaysian adolescents. A total of 797 multi-ethnic Malaysian secondary school student participated in this cross-sectional study. Data was collected two weeks prior to final year examination. A validated Cohen Perceived Stress Scale questionnaire was used to assess the stress level with subsample analysis of 261 participants’ saliva cortisol level. A validated Child Eating Behaviour questionnaire was used to explore eating behaviours. There were 29.1% adolescents having high stress with the mean saliva cortisol 3.8 nmol/L. A positive correlation was observed between perceived stress and emotional overeating; stronger among urban (r = 0.32), female (r = 0.31), underweight (r = 0.34) and moderately stressed adolescents (r = 0.24). In addition, a positive correlation was found between perceived stress and food responsiveness; strongest among Malay (r = 0.23), male (r = 0.24), underweight (r = 0.30) and adolescents with high perceived stress (r = 0.24). The perceived stress level prior to exam period affects the emotional eating and external eating patterns of adolescents.