Pre-clinical data suggest that mutations in the MEN1, DAXX, and/or ATRX genes may potentially increase radiation efficacy in cancer cells. Herein, we explore the association between response to peptide receptor radionuclide therapy (PRRT) and those mutations in patients with gastroenteropancreatic neuroendocrine tumors (GEP-NETs). We analyzed tissue-based next generation sequencing (NGS) assay results and clinicopathologic data from 28 patients with GEP-NETs treated with PRRT. Findings were correlated with progression-free survival (PFS) and objective response (ORR). Patients with mutations in MEN1, DAXX, and/or ATRX (n = 13) had a longer median PFS (26.47 vs. 12.13 months; p = 0.014) than wildtype (n = 15) patients when adjusted for surgery prior to PRRT, tumor grade, and presence of TP53 mutation. Alterations in MEN1 along with a concurrent mutation in either DAXX or ATRX (n = 6) trended towards longer PFS compared to patients without concurrent mutations (31.53 vs. 17.97 months; p = 0.09). ORR was higher in patients with a mutation in MEN1, DAXX, or ATRX (41.67% vs. 15.38%). In pancreatic NET patients, these target mutations also showed a longer PFS (28.43 vs. 9.83 months; p = 0.04). TP53 alterations showed a shorter PFS than wild-type cases (11.17 vs. 20.47 months; p = 0.009). Mutations in MEN1/DAXX/ATRX are associated with improved PFS in patients with GEP-NETs receiving PRRT and might be used as a biomarker for treatment response.