Although vaccination and post-vaccination studies have gained considerable importance in the field of aquaculture diseases, little is understood about the mechanism of immune-protection in vaccinated fish following infection. In the present study, an attempt was made to discover the mechanism of protection rendered by a modified adjuvant-based recombinant outer membrane protein R (rOmpR) vaccine, in rohu, Labeo rohita (an important Indian major carp species) following a challenge with Aeromonas hydrophila. For this, expression analysis of an array of immune molecules (IgM, complement factor 3, interleukin 1β, interleukin 6, tumor necrosis factor α, interleukin 15, MHC I and MHC II) was carried out in the anterior kidney tissues of vaccinated fish, at 0, 12, 24, 48, 72 and 120 h post-challenge. Higher transcript levels of IgM, MHC I and MHC II were evident in the mineral oil-based OmpR vaccinated and modified adjuvant-based OmpR-vaccinated groups, at different time points post-challenge, including the non-challenged fish. Early onset of pro-inflammatory cytokines and expression of most of the immune genes was more pronounced in vaccinated fish at different time points post-challenge, thus indicating a better immune response in these fish. This study indicated the activation of both humoral and cell mediated immunity in vaccinated rohu following a challenge with A. hydrophila.