Mental health problems are increasing among children and adolescents. School-based mindfulness interventions are gaining popularity worldwide and may be a way to decrease depression and anxiety symptoms in students. However, before introducing large-scale mindfulness interventions in school settings, more research is needed on feasible, easily applicable practices that are possible to fit in the school schedule. In this controlled intervention study, a total of 1399 students aged 9-16 were included. The 10-week classroom-based mindfulness intervention comprised daily, brief mindfulness sessions led by school-teachers or via audio files. Symptoms of depression and anxiety were evaluated with Beck scales prior to and after the intervention. In addition to whole group analyses, subgroup analyses on age, sex as well as mode of delivery were performed. ClinicalTrials.gov ID: NCT03327714. No significant differences between the intervention and control group in change of depression or anxiety symptoms after the intervention were detected. However, the subgroup of students who received teacher-led mindfulness sessions (16%) had a significant decrease of depression and anxiety symptoms after 10 weeks compared to those who received the sessions via audio files. Brief mindfulness sessions on daily basis did not have any detectable overall effect on depression and anxiety symptoms among schoolchildren. Our findings do not support an introduction of large-scale mindfulness interventions in schools although the potential influence of mode of delivery needs to be further examined.