Children's mental health is deteriorating while access to child and adolescent mental health services is decreasing. Recent UK policy has focused on schools as a setting for the provision of mental health services, and counselling is the most common type of school-based mental health provision. This study examined the longer-term effectiveness of one-to-one school-based counselling delivered to children in UK primary schools. Data were drawn from a sample of children who received school-based counselling in the UK in the 2015/16 academic year, delivered by a national charitable organisation. Mental health was assessed at baseline, immediately post-intervention, and approximately 1 year post-intervention, using the Strengths and Difficulties Questionnaire (SDQ) completed by teachers and parents. Paired t tests compared post-intervention and follow-up SDQ total difficulties scores with baseline values. Propensity score matching was then used to identify a comparator group of children from a national population survey, and linear mixed effects models compared trajectories of SDQ scores in the two groups. In the intervention group, teacher and parent SDQ total difficulties scores were lower at post-intervention and longer-term follow-up compared to baseline (teacher: baseline 14.42 (SD 7.18); post-intervention 11.09 (6.93), t(739) = 13.78, p < 0.001; follow-up 11.27 (7.27), t(739) = 11.92, p < 0.001; parent: baseline 15.64 (6.49); post-intervention 11.90 (6.78), t(361 = 11.29, p < 0.001); follow-up 11.32 (7.19), t(361) = 11.29, p < 0.001). The reduction in SDQ scores was greater in the intervention compared to the comparator group (likelihood ratio test comparing models with time only versus time plus group-by-time interaction: χ2 (3) = 24.09, p < 0.001), and model-predicted SDQ scores were lower in the intervention than comparator group for 2 years post-baseline. A one-to-one counselling intervention delivered to children in UK primary schools predicted improvements in mental health that were maintained over a 2 year follow-up period.