Insufficient physical activity and growing obesity levels among Malaysian adolescents are becoming a public health concern. Our study is to identify the trends of self-reported physical activity (PA) levels, blood lipid profiles, and body composition (BC) indices from a cohort of 820 adolescents. The self-reported PA was assessed using a validated Malay version of the PA Questionnaire for Older Children (PAQ-C). Fasting blood samples were collected to investigate their lipid profiles. Height, weight, waist and hip circumferences as well as body fat percentage were measured. The baseline and the first follow-up were conducted in 2012 and 2014, respectively. A downward trend in the PA level was seen in all categories with a significant reduction among all rural adolescents (P = 0.013) and more specifically, PA among girls residing in rural areas dropped significantly (P = 0.006). Either a significant reduction in high-density lipoprotein (HDL) or a significant increment in BC indices (i.e., body mass index [BMI], waist circumference [WC], hip circumference, and body fat percentage [BF %]) were seen in this group. Female adolescents experienced more body fat increment with the reduction of physical activity. If not intervened early, adolescents from rural areas may increase their risk of developing cardiovascular diseases earlier.