ATP-competitive Fibroblast Growth Factor Receptor (FGFR) kinase inhibitors, including BGJ398 and Debio1347, show antitumor activity in patients with intrahepatic cholangiocarcinoma (ICC) harboring activating FGFR2 gene fusions. Unfortunately, acquired resistance develops and is often associated with the emergence of secondary FGFR2 kinase domain mutations. Here, we report that the irreversible pan-FGFR inhibitor, TAS-120, demonstrated efficacy in four patients with FGFR2-fusion-positive ICC who developed resistance to BGJ398 or Debio1347. Examination of serial biopsies, circulating tumor DNA (ctDNA), and patient-derived ICC cells revealed that TAS-120 was active against multiple FGFR2 mutations conferring resistance to BGJ398 or Debio1347. Functional assessment and modeling the clonal outgrowth of individual resistance mutations from polyclonal cell pools mirrored the resistance profiles observed clinically for each inhibitor. Our findings suggest that strategic sequencing of FGFR inhibitors, guided by serial biopsies and ctDNA, may prolong the duration of benefit from FGFR inhibition in patients with FGFR2 fusion-positive ICC.