Wild and farm-raised fish can be simultaneously exposed to different types of pathogens in their habitats. Hence, it is important to study their effects, whether isolated or in combination. Therefore, the aim of this study was to evaluate the effects of Lactobacillus pentosus PL11 on the transcription of specific cytokine genes related to immune response, using Japanese eel macrophages as an in vitro model. Head kidney leukocytes were isolated from Japanese eels and cell viability was determined using an MTT reagent. In addition, the Griess reagent was used to determine the nitric oxide (NO) production while, an enzyme-linked immunosobent assay (ELISA) and a quantitative polymerase chain reaction (qPCR) were utilized to quantify the level of proinflammatory cytokines. The results of the study indicated that infection by Edwardsiella tarda alone causes a higher rate of cell death and an increase in the production of proinflammatory cytokines, such as interleukin-1β (IL-1β, 822.67 ± 29.48 pg mL−1), interleukin-6 (IL-6, 13.57 ± 0.55 pg mL−1), and tumor necrosis factor-α (TNF-α, 2033.67 ± 84.68 pg mL−1). However, co-culture with L. pentosus PL11 downregulates the production of NO and the related IL-1β, IL-6, and TNF-α by 46%, 88.4%, 59%, and 77%, respectively. Quantification of the mRNA expression level revealed it to be consistent with the ELISA analysis. Hence, we infer that L. pentosus PL11 plays a significant role in the immunmodulation of the inflammatory responses that arise in fish owing to infection by pathogenic bacteria such as Edwardsiella tarda.