Objective: To investigate the killing effect of 5-fluorouracil (5-FU) loaded polycaprolactone nanoparticles on human cholangiocarcinoma cells in vitro, and its safety and mechanism. Methods: The 5-FU loaded polycaprolactone nanoparticles (5-FU-PCL-NPs) were prepared by ultrasonic emulsification. In vitro hemolysis of the empty nanoparticles and drug release of 5-FU-PCL-NPs was observed, and the inhibition of proliferation and induction of apoptosis of 5-FU-PCL-NPs in human cholangiocarcinoma Hccc-9810 cells were determined. Results: The 5-FU-PCL-NPs were successfully synthesized, with drug loading rate of 15.1% and encapsulation efficiency of 41.9%. The empty nanoparticles showed a negative result in hemolysis test. 5-FU-PCL-NPs exhibited a sustained 5-FU release and the 72-h release rate was 62.9%. Compared with pure 5-FU, 5-FU-PCL-NPs had a significantly increased inhibitory effect on proliferation in Hccc-9810 cells, significantly decreased IC50 value [(1.32±0.12) μg/mL vs. (2.5±0.39) μg/mL], and significantly enhanced effect on apoptosis in Hccc-9810 cells (all P<0.05). The empty nanoparticles exerted no obvious effect on apoptosis in Hccc-9810 cells (P>0.05). Conclusion: The 5-FU loaded polycaprolactone nanoparticles (5-FU-PCL-NPs) possess a sustained-release property that prolongs the suppressive effect of 5-FU, and have enhanced killing effect on human cholangiocarcinoma cells in vitro, with a satisfactory biological safety profile.