Indonesia is one of the world’s largest fresh pepper (Capsicum spp.) fruit-producing countries, and hot peppers are essential spices in Indonesian cuisine. During the last two decades, begomovirus, which is transmitted by the whitefly, Bemisia tabaci (Gennadius), and causes pepper yellow leaf curl disease, began to cause a huge economic loss by damaging pepper plants in Indonesia. In the present study, a highly efficient inoculation method was established for Pepper yellow leaf curl Indonesia virus (PepYLCIV), the most infectious bipartite begomovirus in pepper plants cultivated in North Sumatra, by combining agroinoculation and subsequent grafting. Partial tandem repeats of PepYLCIV DNA A and B were constructed and cloned into a binary pGreenII vector, and their infectivity was tested. Co-inoculation of Nicotiana benthamiana L. and Solanum lycopersicum L. ‘Momotaro’ with PepYLCIV DNA A and DNA B resulted in the production of typical begomoviral symptoms. Both the injection of the cotyledons with cultured agrobacteria and the inoculation of the hypocotyl with agrobacterial colonies induced viral symptoms in pepper No. 218 (C. annuum L.) seedlings in approximately 55–75%. When agroinoculated symptomatic No. 218 was grafted onto an uninfected ‘Takanotsume’ (C. annuum), all newly elongated shoots from the rootstock of ‘Takanotsume’ produced typical begomoviral symptoms. Agroinoculation combined with subsequent grafting provides a highly efficient method for introducing PepYLCIV into pepper plants.