Background: Recent investigation in pancreatic adenocarcinoma (PDAC) demonstrates an association of molecular subtype with chemosensitivity and prognosis. TP53 and GATA6 are two genes independently associated with worse survival in PDAC. Here, we evaluated treatment outcome by genetic alterations of TP53 and GATA6 among patients with pancreatic cancer across New York’s largest health care system. Methods: This is a retrospective analysis of patients at Northwell Health diagnosed with PDAC between 2014 to 2021. Surgical status was used to segregate patients into two groups: resected and unresected. TP53 and GATA6 mutation status was compared for disease-free survival (DFS) (resected) or progression-free survival (PFS) (unresected), and for overall survival (OS). Additionally, patient survival by type of chemotherapy administered was evaluated. The Kaplan–Meier method was used to determine overall survival (OS), and the Wilcoxon test was used to compare survival curves. Results: Tumor mutational profiling data were available for 129 patients. TP53 mutations were found in 105 patients (81.4%), GATA6 amplifications were found in 18 patients (14.0%), and 16 patients had both mutations. TP53 mutations were associated with a worse OS compared to the wild-type TP53 population (n = 24) (median OS 22.7 months, 95% CI 12.5 to 41.1, vs. 44.3 months, 95% CI 24.5 to 80.3, HR 1.97, p = 0.048). Among patients with a TP53 mutation, a survival advantage was observed in those who had a GATA6 amplification compared to those who did not (median OS 25.5 months, 95% CI 10.9 to 44.6, vs. 22.1 months, 95% CI 12.6 to 51.5, HR 1.68, p = 0.038). In patients with unresected PDAC, the survival advantage of GATA6 amplification within TP53 mutated group was more prominent than the absence of the amplification (median OS 23.8 months, 95% CI 10.0 to 56.5, n = 12 vs. 10.5 months, 95% CI 4.4 to 24.8, n = 55, HR 0.52, p = 0.008). In the TP53 mutation group, among 33 patients who received Gem/NabP as the first-line chemotherapy, patients with GATA6 amplification (n = 8) had significantly improved survival compared to those without GATA6 amplification (n = 25) (mean OS 23.1 months, 95% CI 8.5 to 63.0, vs. 9.4 months, 95% CI 3.44 to 26.6, HR 0.51, p = 0.027). Conclusions: Genetic mutations in TP53 were associated with shorter OS than wild-type TP53. Contrary to our initial expectation that co-mutation would be associated with even worse survival, we found that GATA6 amplification appeared to attenuate poor prognosis observed in TP53-mutant patients. Additionally, GATA6 amplification may be a predictive marker for better responses to Gem/NabP chemotherapy.