Cholangiocarcinoma (CCA) is an aggressive and lethal malignancy with limited therapeutic options. Despite recent advances in diagnostic imaging for CCA, the early diagnosis of CCA and evaluation of tumor invasion into the bile duct and its surrounding tissues remain challenging. Most patients with CCA are diagnosed at an advanced stage, at which treatment options are limited. Molecular imaging is a promising diagnostic method for noninvasive imaging of biological events at the cellular and molecular level in vivo. Molecular imaging plays a key role in the early diagnosis, staging, and treatment-related evaluation and management of cancer. This review will describe different methods for molecular imaging of CCA, including nuclear medicine, magnetic resonance imaging, optical imaging, and multimodal imaging. The main challenges and future directions in this field are also discussed.