We investigated how adolescents’ time allocation across daily activities influences their body mass index and well-being by paying explicit attention to gender and activities relevant to low- and middle-income countries (LMICs). We hypothesized that the inequitable domestic burden shouldered by girls adversely affects their health and well-being. Using data from three waves of the Young Lives Longitudinal Survey (2009, 2013, and 2016) tracking 1891 children aged 8, 12, and 15 from predominantly rural, low-income households from South India, we analyzed gendered time use patterns and their implications. Girls spent more time on caregiving, housework, and studying at home, while boys allocated more time to school, leisure, and sleep. Random effects models revealed that time spent on caregiving and housework increased the likelihood of being overweight or obese among girls, whereas leisure time reduced it. Time in school was positively associated with girl’s thinness, as was time spent on sleep for both boys and girls. Gender moderated the effects of time spent on housework and unpaid economic tasks on thinness, reducing its likelihood for girls. Subjective well-being improved with time spent in school and studying for all adolescents. Fixed effects models revealed it worsened for girls engaged in paid work and boys engaged in leisure. Longer sleep hours improved boys’ well-being. These findings underscore that gendered time use patterns, particularly girls’ unequal burden of domestic responsibilities, contribute to their increased risk of overweight and obesity. Addressing these disparities is crucial for improving adolescents’ health and well-being in resource-poor settings in LMICs.