This is a case study that assessed risk factors for transmission of red sea bream iridovirus (RSIV) focused on cross-contamination of aquaculture equipment in semi-open system aquaculture. Our investigation during the RSIV outbreak in the fish farm demonstrated that equipment used for collecting dead fish, such as landing nets and gloves, was highly contaminated with RSIV. Based on the results, a daily operation for collecting dead fish was implemented, starting with net pens where no disease occurred, followed by the net pen where the RSIV outbreak occurred to prevent fomite transmission via RSIV-contaminated equipment. In addition, the landing nets used for collecting dead fish were disinfected at the end of each day to avoid carryover of the virus to the following day. RSIV was not transmitted to the other net pens in the fish farm for more than 30 days. However, once an RSIV outbreak occurred in the net pen that was upstream in the operation for collecting dead fish, RSIV was transmitted to all net pens in approximately 1 week, implying that the transmission was caused by cross-contamination. This study suggested that appropriate hygiene management is important to prevent fomite transmission between net pens, even in semi-open system aquaculture.