Social anxiety is common in childhood and potentially transitions into clinical disorders including depression. The present study aimed to examine the effectiveness of an indicated prevention program for children screened in routine care. Data came from the PROMPt project, a prospective implementation study (10/2018-09/2022) that explored a novel care chain, starting with screening with the Strengths and Difficulties Questionnaire (SDQ) as part of regular health check-ups, followed by indicated assignment and participation in a prevention program. Questionnaires assessing anxiety and depression symptoms were administered shortly after screening or before program participation (T0), six months after screening or after program participation (T1) and at a follow-up, six months after T1 (T2). Children who participated in a group cognitive-behavioral social skills program (TT; n = 145) were compared using mixed model analyses with non-participating children who were either screened as normal (NOR; n = 894) or refused program participation despite indication (NoTT; n = 67). TT scores improved from T0 to T1 compared to NOR and NoTT (anxiety β = -0.71 and β = -0.71, social anxiety β = -0.46 and β = -0.52, depression β = -0.52 and β = -0.73). Improvement was maintained at T2. Moderation analyses showed a trend toward greater benefit for participants with higher baseline scores. Indicated prevention can improve anxiety and depression symptoms in children identified by screening in routine care. Systematic screening and targeted prevention may positively affect mental health of children on a population level.