The mechanisms of behavior change in youth screen-time interventions are poorly understood. Participants were 361 adolescent boys (12-14 years) participating in the ATLAS obesity prevention trial, evaluated in 14 schools in low-income areas of New South Wales, Australia. Recreational screen-time was assessed at baseline, 8- and 18-months, whereas potential mediators (i.e., motivation to limit screen-time and parental rules) were assessed at baseline, 4- and 18-months. Multi-level mediation analyses followed the intention-to-treat principle and were conducted using a product-of-coefficients test. The intervention had a significant impact on screen-time at both time-points, and on autonomous motivation at 18-months. Changes in autonomous motivation partially mediated the effect on screen-time at 18-months in single and multi-mediator models [AB (95% CI) = -5.49 (-12.13, -.70)]. Enhancing autonomous motivation may be effective for limiting screen-time among adolescent males.Australian New Zealand Clinical Trials Registry No: ACTRN12612000978864.