Various cases of gastrointestinal stromal tumor (GIST) coinciding with other gastrointestinal malignancies have been reported to date, however, the synchronous occurrence of GIST and intrahepatic cholangiocarcinoma (ICC) is exceptionally rare and, to the best of our knowledge, has only been reported once. The coinciding malignancy has usually been encountered incidentally during surgical exploration. Thus, this is the first report where a targeted biopsy of the clinically suspicious lesion was used to determine the diagnosis of ICC concurrent with GIST. The liver is the most frequent metastatic site of GIST, therefore, additional hepatic masses may be mistakenly diagnosed as metastatic disease, rather than the presentation of multiple primary tumors. This subsequently delays the accurate diagnosis and complicates the performance of a curable resection. The current study reports a case of advanced synchronous GIST and ICC, which was operable at initial presentation, but progressed to become surgically unresectable.