Background Aberrant fibroblast growth factor receptor (FGFR) signaling drives the growth of many bladder cancers. NVP-BGJ398 is a small molecule with potent inhibitory activity of FGFRs 1, 2, and 3, and has been shown to selectively inhibit the growth of bladder cancer cell lines that over-express FGFR3 or have oncogenic FGFR3 fusions. As with many agents targeting receptor tyrosine kinases, resistance is known to develop. Objective We sought to identify potential mechanisms of resistance to NVP-BGJ398 in cell culture models of bladder cancer. Methods RT-112 bladder cancer cell lines were derived that were resistant to growth in 3uM NVP-BGJ398. RNA-sequencing was performed on resistant and parental cell lines to identify potential resistance mechanisms and molecular experiments were carried out to test these predictions. Results RNA-seq demonstrated decreased expression of FGFR3 and increased expression of FGFRs 1 and 2 in resistant cell lines. Over-expression of FGFR3 in NVP-BGJ398 resistant cells decreased their proliferation. Pathway analysis of RNA-seq data also implicated PIM kinase signaling, among other pathways, as a potential mediator of resistance. Treatment of BGJ398 resistant cells with the PIM kinase inhibitor SGI-1776 reduced the growth of the cells. Conclusions Our results suggest that altered FGFR expression and PIM kinase activity could mediate resistance to NVP-BGJ398. These pathways should be investigated in samples from patients resistant to this drug.