Using self-determination theory (SDT) as an explanatory framework, this randomised-controlled study evaluates the effect of a motivational interviewing (MI)-based intervention as an addition to a standard weight loss programme (SWLP) on physical activity (PA) practice in obese adolescents over a six-month period. Fifty-four obese adolescents (mean age = 13 years, mean BMI = 29.57 kg/m²) were randomly assigned to an SWLP group (n = 28) or SWLP + MI group (n = 26). Both groups received two SWLP sessions, supplemented for the SWLP + MI group, by six MI sessions. Perceived autonomy support, perceived competence, motivational regulations, PA and BMI were assessed at baseline, three and six months (i.e. the end of the programme). MLM analyses revealed that compared to SWLP, the SWLP + MI group had a greater BMI decrease and a greater PA practice increase over time. Moreover, the SWLP + MI group reported greater autonomy support from medical staff at the end of the programme, greater increase in integrated and identified regulations and a stronger decrease in amotivation. MI appears as an efficient counselling method as an addition to an SWLP to promote PA in the context of pediatric obesity.