Hirame novirhabdovirus (HIRRV) is a severe viral pathogen of flounder resulting in significant losses to the aquaculture industry. However, the mortality due to the disease would be significantly reduced when the water temperature was increased from 10 to 20 °C. In this study, we examined the potentiality of vaccination with live HIRRV under a temperature-controlled culture condition for development of protective immunity in flounder. Flounders were infected with HIRRV at 10 °C and maintained for 2 days, and then the temperature was shift up to 20 °C. When the temperature was further shift down to 10 °C at 7 (S-7 group), 14 (S-14 group) or 21 (S-21 group) days post infection (dpi), mortality rates of 60%, 13.33% and 0 were observed, respectively. To investigate the development of protective immunity of survived flounder, a re-challenge was performed and a highest survival rate of 80% was found in S-21 group, which was significantly higher than S-14 group (65%) and S-7 group (45%). Moreover, it was found that a lower viral load was detected in the flounder maintained at 20 °C for a longer time, and a longer maintaining of survived flounder at 20 °C would also elicit higher percentages of IgM + B lymphocytes and specific antibodies levels. Notably, a significantly higher levels of specific antibodies were detected post re-challenge compared with the first peak level after initial infection. Therefore, these demonstrated that the initial infection with live HIRRV under a temperature-controlled condition elicited an effective protective immune response against HIRRV, and maintaining at 20 °C for a long enough time would allow the HIRRV-infected flounder to eliminate the virus completely and acquired a protective immunity against HIRRV infection. This is the first study showing the possibility of developing an effective preventive measure against HIRRV by vaccination with live virus under controlled water temperature.