Pharmacokinetic (PK) study of medicinal herbs is a great challenge, because which component(s) is(are) the bioactive ingredients is largely unknown. Most of the reported PK studies of herbs focused on the major ingredients regardless of their in vivo bioactivities, while PK of components with low content in herbs is often ignored. The present study demonstrates how PK study can reveal potential importance of a low content ingredient to the herbal bioactivities using Z-butylidenephthalide (BuPh), a bioactive phthalide present in a significantly low quantity in medicinal herb Chuanxiong Rhizoma, as an example. PK of BuPh was investigated in rats using Chuanxiong extract, fraction containing BuPh and ligustilide, and pure BuPh, respectively. The results demonstrated that remarkable blood concentrations of BuPh were observed after administration of the herbal extract and its systemic exposure was significantly different between BuPh given in pure and mixed forms. More interestingly, AUC of BuPh via intake of fraction (9.3-fold) and extract (4.5-fold) was significantly greater than that obtained from pure BuPh, which was further evidenced to be mainly due to metabolic conversion from ligustilide, a major component in Chuanxiong. Our findings revealed that although it naturally occurred in low amount, BuPh reached significant systemic concentrations via metabolic conversion from ligustilide. Moreover, our results demonstrated that PK study is one of crucial and inevitable steps for revealing in vivo bioactive ingredients of herbal medicines, and such studies should be more appropriate to focus on in vivo profile of the ingredients co-existing in herbs rather than only studying them individually.