Clivorine is an otonecine-type pyrrolizidine alkaloid (PA) isolated from the Chinese medicinal plant Ligularia hodgsonii Hook., and our previous reports have shown its toxicity on human normal liver L-02 cells. It is generally believed that biotransformation of PAs to its metabolites is required for their toxicity; thus, there is nearly no report about the toxicity of clivorine on other non-hepatic cells in vitro. The aim of this study is to observe the toxicity of clivorine on the non-hepatic human embryonic kidney 293 (HEK293) cell that is of epithelial origin, and its primary mechanism. Our results showed that clivorine significantly reduced HEK293 cell viability, but there was no detectable apoptotic DNA ladder and cleaved fragments of caspase-3 and caspase-9 in clivorine-treated cells, which indicates the toxicity of clivorine is not due to inducing apoptosis. The results of western blot showed that clivorine induced sustained p38, c-Jun N-terminal kinase (JNK) and extracellular signal-related kinases (ERK1/2) phosphorylation in a concentration- and time-dependent manner, and the JNK inhibitor SP600125 significantly augmented the toxicity of clivorine. Our results suggest that clivorine itself has direct toxicity on HEK293 cells, and phosphorylated JNK may play some role in counteracting the toxicity of clivorine on HEK293 cells.