With the current researches on replacing antibiotics with different dietary interventions, bacteriophages (BP) are potential antimicrobial intervention because of their ability to affect specific bacteria. A study was conducted to evaluate the role of BP against Salmonella enterica serovar Enteritidis (SE) on SE internal organs colonization and ileum immune response in laying hens. Hens were challenged both orally and intracloacally with 108 cfu/mL cells of nalidixic acid resistant Salmonella Enteritidis (SENAR). Thirty-two Single Comb White Leghorns were randomly allocated to 4 dietary treatments: 1) unchallenged control (negative control; T1), 2) SENAR challenged control (positive control; T2), 3) SENAR challenged + 0.1% BP (T3), and 4) SENAR challenged + 0.2% BP (T4). The number of SENAR in the ceca was significantly reduced by 0.2% BP supplementation (P < 0.05) at 7 d post infection (dpi). The respective number of SENAR was reduced from 2.9 log cfu/gm in T2 and T3 to 2.0 log cfu/gm in T4. There was no significant effect of T3 on reduction of numbers of cecal SENAR. A significant reduction of SENAR was observed in the liver with gall bladder (LGB) from 0.75 in T2 to 0.18 log cfu/gm in T4. In the spleen, T4 significantly reduced (P < 0.05) SENAR to 0.56 log cfu/gm compared to T2 and T3 (0.94 log cfu/gm). There was no significant effect of T3 in reduction of prevalence of spleen SENAR. By supplementing 0.2% BP (T4), the SENAR in the ovary was reduced to 0 log cfu/gm. There was a significant reduction (P < 0.05) in fecal SENAR at 6 dpi by T4 (0.71 log cfu/gm) compared to the positive control (1.57 log cfu/gm). The expression of interferon (IFN)-Γ, interleukin (IL)-6, and IL-10 was significantly increased in the ileum by SENAR challenge compared to the negative control. This study suggests that apart from commonly used prebiotics or probiotics, BP are pathogen-specific and can be used as one of the dietary strategies to reduce SE colonization and induce immune modulation in laying hens.