Gemcitabine is a cornerstone chemotherapeutic for pancreatic ductal adenocarcinoma (PDAC); however, the frequent development of resistance compromises its efficacy and poses a significant challenge to patient prognosis. Here, we report that nuclear pore protein NUP93 is upregulated in PDAC and correlates with poor patient survival. Functional studies demonstrated that NUP93 promotes PDAC cell proliferation and confers gemcitabine resistance by enhancing DNA damage repair. Mechanistically, NUP93 interacts with the transcription factor SOX2 by recognizing its nuclear localization sequence and facilitates its nuclear import. Nuclear SOX2 transcriptionally activates the key stress granule component G3BP1 by directly binding to its promoter. Subsequently, G3BP1 stabilizes the mRNA of RAD51, a crucial homologous recombination repair factor, thereby promoting DNA damage repair and gemcitabine resistance. In vivo, disruption of the NUP93/SOX2/G3BP1 axis suppressed tumor growth and synergized with gemcitabine. Our findings unveil the novel NUP93-SOX2-G3BP1 signaling axis as a critical driver of gemcitabine resistance in PDAC, presenting a promising therapeutic target for overcoming chemoresistance.