Background: Emerging evidence underscores the pivotal role of long non-coding RNAs (lncRNAs) as master regulators of oncogenic pathways, positioning them as compelling therapeutic targets in precision oncology. While the natural flavonoid quercetin has demonstrated potent anti-neoplastic activity against non-small cell lung cancer (NSCLC), its influence on lncRNA-mediated oncogenic pathways remains unknown. This study is designed to elucidate whether quercetin exerts its anti-NSCLC effects via modulation of lncRNA just proximal to XIST (JPX) and its downstream signaling axis. Methods: NSCLC cell lines were treated with quercetin, and functional assays (CCK-8, BrdU incorporation, scratch assay, and Transwell migration) were conducted to assess proliferation and metastatic potential. Gain- and loss-of-function experiments, combined with qPCR and western blotting, were performed to validate the JPX-modulated regulatory network. Results: Quercetin significantly suppressed NSCLC proliferation and migration by downregulating oncogenic JPX, which in turn upregulated tumor-suppressive miR-495-3p, leading to bromodomain-containing protein 4 (BRD4) suppression. JPX silencing mimicked quercetin’s effects, while rescue experiments confirmed the JPX/miR-495-3p/BRD4 axis as critical for quercetin’s activity. Conclusion: Our findings identify quercetin as a natural compound targeting the JPX-miR-495-3p-BRD4 cascade, providing both mechanistic insights and a translational rationale for quercetin-based NSCLC therapy. These findings highlight the therapeutic potential of quercetin in NSCLC and support further exploration of lncRNA-targeted strategies.