Background: Over 10% of the 610,000 homeless persons in the United States are veterans. Homelessness is associated with more substance abuse and mental health diagnoses, and higher hospitalization rates. We assessed the mental health (MH) and substance abuse (SA) burden and use of outpatient MH and SA resources in a homeless veteran population. Methods: Electronic medical record data were obtained on all homeless patient aligned clinic team (HPACT) and non-homeless patients during fiscal years 2016 and 2017. MH and SA prevalence and related outpatient resource use were compared in three sub-populations: HPACT patients, non-HPACT patients with a homelessness ICD-10 code, and non-homeless PACT patients. Chi-square analyses and t-testing were performed to identify between-group differences during the fiscal year 2018. Results: HPACT and homeless, non-HPACT patients had higher MH and SA disorder prevalence, and MH/SA comorbidity in both years (p < 0.001) with few significant changes from year 1 to year 2. PTSD clinic utilization among patients with PTSD increased from year 1 to year 2 for HPACT, non-HPACT homeless, and non-homeless patients (25% vs. 4%, 25.9% vs. 16.7%, 34% vs. 25.2%, p < 0.01) with the greatest improvement among HPACT patients. Overall, outpatient MH service use increased from year 1 to year 2, among patients with an MH diagnosis (77.3% vs. 44.3%, 82.7% vs. 54.2%, 69% vs. 51.4%, p < 0.001), with greater improvement in the HPACT and non-HPACT homeless patients. For those with an SA diagnosis, outpatient utilization rates doubled (52.5% vs. 27%, 57.5% vs. 27.7%, 35.2% vs. 17.9%, p < 0.001). HPACT and non-HPACT homeless patients were more likely to have a psychiatric hospitalization in years 1 and 2 compared with non-homeless patients (5.8%/6.1% vs. 6.7%/4.9% vs. 1.1%/1%, p < 0.001). There was no change in psychiatric hospitalization rates from year 1 to year 2. Conclusions: More research on MH and SA treatment strategies is needed to address the significant disease burden among homeless veterans.