Radiotherapy for organ preservation has increased in popularity over enucleation in the modern management of choroid melanoma (CM). However, it is unknown whether eye plaque brachytherapy or proton external beam radiotherapy have equivalent outcomes. Demographic and clinical data for 1224 patients with histologically confirmed choroid melanoma treated with either brachytherapy or proton beam therapy from 2004-2013 were obtained from the National Cancer Database (NCDB). Patients were excluded if tumor thickness and basal diameter were not recorded. Patients were staged T1-4N0M0 from the recorded tumor dimensions according to AJCC 7th edition. Logistic regression and propensity score matching was used to create a 1:1 matched cohort. Kaplan-Meier and Cox regression analyses were performed to evaluate survival in brachytherapy and proton groups with and without propensity score matching. Log rank was used to compare survival. Median follow up was 37 and 29 months for brachytherapy and protons, respectively, and 93% of patients were treated from 2010-2013. The majority of patients were treated with brachytherapy (n = 996) vs. protons (n = 228). There were no differences in age (61 years), sex, insurance status, Charlson-Deyo score, T stage, ciliary/extraocular extension, or tumor diameter or thickness. Patient receiving protons were more likely to be treated at an academic center (99 vs. 76%), non-white (86 vs. 96%), travelled >60 miles to treatment (81 vs. 72%), started treatment > 60 days from diagnosis (19 vs 11%); Proton patients also came from more urban, affluent and educated zip codes (all p < 0.004). Median proton dose was 56 Gy in 4 fractions. Two year overall survival was 96% vs. 92%, and 5 year overall survival was 81 vs. 54% for brachytherapy and protons, respectively (p < 0.001). Cox regression found older age (HR = 1.05), larger tumor diameter (12-18mm, HR = 2.25, >18mm, HR = 3.56), academic facility (HR = 2.07), and protons (HR = 1.91) were negative prognosticators of survival (all p <0.02). In the propensity-score matched cohort, two year overall survival was 97% vs. 93%, and 5 year overall survival was 77% vs. 51% for brachythreapy and protons, respectively (p = 0.008). Cox regression found older age (HR = 1.06), larger tumor diameter (12-18mm, HR = 2.48, >18mm, HR = 6.41), and protons (HR = 1.89) were negative prognosticators of survival (all p <0.02). Treatment with protons is associated with inferior survival outcomes compared to brachytherapy in this retrospective analysis. There may be unaccounted variables not reported to the NCDB that influence survival, necessitating further prospective research.