One of the obstacles to controlling rodents on livestock farms in Japan is the lack of information about characteristics that lead to infestations. To address this knowledge gap, we performed a nationwide survey that collected information from livestock farmers, including the types and number of livestock present, severity of rodent infestation, rodent management approaches utilized, and details about the most- and least-infested barns. More than 80% of respondents reported rodent infestation on their farms, especially rodents observed on overhead beams and girders. A multiple ordinal logistic regression analysis revealed that the odds ratio of rodent infestation was higher on farms housing pigs and lower on farms with chickens, as compared to farms with cattle. We also found that medium-sized farms, but not large-sized farms, showed a higher odds ratio than small-sized farms. Furthermore, the odds ratio was similarly higher on farms that implemented rodent control measures by themselves or with the assistance of pest control operators, compared to farms with no rodent management. Within a farm, barn age contributed to infestation status, such that the most-infested barns were older than the least-infested barns, regardless of livestock species. Furthermore, the proportion of ad libitum feeding was higher in the most-infested barns than in the least-infested barns on pig farms. Taken together, our results provide valuable information for understanding rodent infestations on livestock farms in Japan, which can contribute to the development of better management approaches.