Vaccination rates for mumps, measles, and rubella (MMR) and tetanus, diphtheria, pertussis, and polio (Tdap‐IPV) fall short of global targets, highlighting the need for vaccination interventions. This study examines the effectiveness of a city‐wide school‐based educational vaccination intervention as part of an on‐site vaccination program aimed at increasing MMR and Tdap‐IPV vaccination rates versus on‐site vaccination alone among sociodemographically diverse students from Berlin, Germany. The study was a 1:1 two‐arm cluster randomized controlled trial, with schools randomly assigned to either the Educational Class Condition (ECC) or the Low‐Intensity Information Condition (LIIC). Both received an on‐site vaccination program, while students in the ECC received an additional educational unit. Primary outcomes were MMR and Tdap‐IPV vaccination rates. In total, 6512 students from 25 randomly selected urban area secondary schools participated. For students providing their vaccination documents on the day of the intervention (2273, 34.9%), adjusted Poisson mixed models revealed significant between‐group differences in favor of the ECC (MMR: logRR = 0.47, 95%CI [0.01,0.92], RR = 1.59; Tdap‐IPV: logRR = 0.28, 95%CI [0.10,0.47], RR = 1.32). When adjusting for socioeconomic and migration background, between‐group differences became non‐significant for MMR but remained significant for Tdap‐IPV. Findings suggest that educational, school‐based on‐site vaccination appears to be a promising strategy for increasing vaccination uptake in adolescents.