Background: Child psychiatry has enjoyed a long tradition of using brief psychotherapy with children, but research on its efficacy and effectiveness in the setting of routine clinical care is remarkably sparse; the aim of this study was to evaluate the efficacy of an original model of brief psychodynamic psychotherapy (BPP) for children with emotional disorders in a clinical outpatient setting. Methods: A sample of 30 subjects (6.3–10.9 years old) was divided into an experimental BPP group and a control group. Each subject was evaluated at the beginning, after 6 months and at an 18-months follow-up. Outcome measures were Children’s Global Assessment Scale and Child Behavior Check-List. Statistical and clinical significance of change were evaluated. Results: At the first evaluation, the experimental group showed a better improvement in global functioning; at follow-up, the two groups improved to a comparable degree, but only the mean of the experimental group moved to a functional range. The experimental group showed a significant reduction in total behavioral problems and externalizing problems at the follow-up. Conclusions: The better improvement of the experimental group in two outcome measures suggests that BPP is efficient in emotional disorders. The hypothesis that BPP introduces changes at long term (sleeper effects) is suggested. The improvement in global functioning of the two groups is discussed in relation to specific characteristics of emotional disorders. Finally, limitations of the study are discussed and in particular the bias introduced by lack of randomization.