Cultivation of hairy roots is an effective method to get high in plumbagin secondary metabolites. With different genotypes, setting up a stable genetic transformation system is peculiar and difficult. The plumbagin is found in the roots of Plumbago auriculata L., a secondary metabolite with significant medicinal value. Still, the natural root grows slowly, and their accumulation period is lengthy (2–6 years). In this paper, we first explored the most effective Agrobacterium rhizogene-mediated (A4, ATCC 15834, and LBA 9402) genetic transformation to induce hairy root of P. auriculata. We compared the difference of the plumbagin concentration in the root between tissue culture and seedling. The results showed that the leaves were soaked with bacterial solution for 25–30 min and then transferred to 1/2 MS + acetosyringone 100 µM agar solidified medium for 2-5d. After co-culture, we transferred the leaves to 1/2 MS + Cefotaxime sodium of different concentrations sterilized for 7d. Under this scheme, three strains can induce hairy roots, with ATCC 15834 having the highest hairy root transformation efficiency (86.78 ± 0.74%) and the earliest root emergence time (8.33 ± 0.58 d). 1-month-grown hairy root showed an increase in plumbagin compared with the untransformed roots of 1-year-old live seedlings, with ATCC 15834 induced roots having the highest content of 38.95 mg·g−1 DW, which was 72.13 times higher than the untransformed roots and 3.95 times higher than that of 1-year-old live seedlings. This is an important experimental basis for biosynthesis mechanism of plumbagin and the feasibility of subsequent commercial production. A genetic transformation system was established for hairy root of P . auriculata by A. rhizogene. A reliable and rapid method was developed to obtain the plumbagin with high medicinal value.