BACKGROUND: Calcium hydroxide is the most commonly used material in indirect pulp treatment (IPT). However, its drawbacks required its replacement by other materials. AIM: This study aims to estimate clinically and radiographically the success of indirect pulp treatment of young permanent molars with either photo-activated oral disinfection (PAD) or calcium hydroxide. DESIGN: This Randomized Controlled Pilot Trial included 32 vital first permanent molars with deep caries that were treated by indirect pulp treatment with either PAD (group 1) or calcium hydroxide (group 2). Clinical and radiographic success in addition to newly-formed dentin thickness were evaluated regularly at 2, 6, 9, and 12 months. RESULTS: The success for both groups was 100% clinically and radiographically at all follow-up periods. Regarding the mean thickness of newly-formed dentin for both groups at different follow-up periods, there was no statistically significant difference between both groups at 2, 6, 9, and 12 months, with P values = 0.825, 0.146, 0.280, and 0.400, respectively. CONCLUSIONS: The clinical and radiographic success for indirect pulp treatment of young permanent molars with both PAD and calcium hydroxide were comparable.