Objectives This study compares treatment engagement and outcomes between two groups of adolescents with psychiatric and substance use disorders (SUD): one received treatment with Animal Assisted Therapy (AAT) and another without AAT. Methods This is an exploratory study with a quasi-experimental pre-post comparison group design. Participants were 31 adolescents (ages 12-17 years) participating in an urban school-based substance treatment program. Cases (n = 14) received treatment with AAT, whereas comparison (n = 17) received treatment without AAT. The outcome measures included: number of sessions attended, proportion of negative urine drug screens for non-nicotine substances, overall-wellbeing, and the School Engagement Instrument. Student's T test and a Wilcoxon Rank Sum Test were used to evaluate differences. Outcomes that differed significantly between groups were further evaluated using unadjusted linear regression. Results Participants who received treatment with AAT (M = 9.9, SD = 3.2) attended more therapy sessions within a 16week period (β = 3.5, t(1) = 2.89, p = 0.0072) than those that received treatment without AAT (M = 6.4, SD = 3.5). Additionally, the AAT group (Mdn = 2.9, IQR: 1.8, 5.0) had a greater improvement in overall-wellbeing (β = 3.6, t(1) = 3.74, p = 0.0009) than treatment group without AAT (Mdn = 0.5, IQR: −2.6, 1.4). Conclusions AAT could be a way to increase engagement for youth in substance use treatment.