Childhood internalizing problems such as anxiety and depression can have serious personal, familial and societal repercussions, including drug and alcohol abuse, delinquency, unplanned pregnancy, and even suicide. There is little research on mindfulness interventions for children with clinical levels of internalizing problems, and school-based mindfulness research with children has focused on non-clinical groups. We employed a two-stage screening and intervention procedure to evaluate an in-school mindfulness-based cognitive intervention for Hong Kong children with subclinical internalizing difficulties. Ninety-three fourth to sixth graders were screened, and twenty students (age 9–13, median age 10) highest among their peers on internalizing problems, but lowest on externalizing problems, participated in a 9-week group mindfulness-based intervention. We employed a two-phase open trial design, with random assignment to an immediate intervention group or wait-list control group. In single-trial analysis, one-tailed dependent sample t-tests showed significant decreases in both worry and in symptoms of panic disorder, obsessive compulsive disorder, generalized anxiety and overall internalizing problems. In a randomized controlled trial analysis, the immediate intervention group evidenced larger but nonsignificant reductions on almost all measures. Eighty-five percent of the participants rated the program as helpful, and 65–80 % reported improvement in handling emotions and interpersonal relationships at post-treatment, with some treatment gains maintained at 3-month follow-up. These preliminary findings have encouraging implications for implementing time-limited school-based mindfulness interventions targeting elevated childhood internalizing difficulties.