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The mainstay of advanced gastric cancer (GC) therapy is DNA-damaging drugs. Using proteogenomic analysis of a panel of eight GC cell lines, we identified genetic alterations and signaling pathways, potentially associated with resistance to DNA-damaging drugs. Notably, 5-fluorouracil (5FU) resistance was associated with PD-L1 expression, but not established GC subtypes. In publicly available cohort data, PD-L1 expression was associated with a reduced risk of GC progression. In addition to PD-L1, expression of inflammatory genes induced by lymphocyte cytokines was consistently associated with prolonged survival in GC. In our validation cohort, total lymphocyte count (TLC) predicted a better relapse-free survival rate in GC patients with 5FU-based adjuvant chemotherapy than those with surgery alone. Moreover, TLC⁺ patients who had no survival benefit from adjuvant chemotherapy were discriminated by IκBα expression. Collectively, our results suggest that 5FU resistance observed in cell lines may be overcome by host immunity or by combination therapy with immune checkpoint blockade.