RF2a, encoding a bZIP type transcription factor, which is important for rice development is reported to bind to Box II, a crucial cis-element of the RTBV promoter and activate transcription from the RTBV promoter in infected plants. Overexpression of RF2a in transgenic rice had been reported to increase tolerance against the tungro virus. We reported the overexpression of RF2a in transgenic rice plants cultivar IR64. Bioassay using an Indonesian tungro virus isolate indicated that there was a significant increase in the tolerance of the transgenic rice lines compared to the wild-type IR64, and was comparable to the tolerant control Tukad Petanu. qRT-PCR on RF2a-overexpressed transgenic rice and the wild-type control showed that in tungro virus-infected transgenic rice plants in which weak or no RTD symptoms were observed, the relative expression of RF2a were increased. The increase in tolerance toward tungro virus was suggested due to a high level of RF2a in plants that can support rice development amid virus replication. On the contrary, in infected susceptible wild-type plants, in which the level of RF2a was low, severe RTD symptoms were observed. Thus, the availability of RF2a in tungro virus-infected IR64 plants plays an important role in determining the development of RTD symptoms.