Abstract This study analyzed time-dependent effects of vaccination against Y. ruckeri on the oxidative mechanism underlying those effects by detecting relevant lipid peroxidation (2-thiobarbituric acid reactive substances, TBARS) and protein oxidation biomarkers [aldehydic and ketonic derivatives of oxidatively modified proteins (OMP)], antioxidant defenses [activities of superoxide dismutase (SOD), catalase (CAT), glutathione reductase (GR), glutathione peroxidase (GPx), total antioxidant capacity (TAC)], as well as activities of lysosomal functioning [alanyl aminopeptidase (AAP), leucyl aminopeptidase (LAP), acid phosphatase (AcP), and β-N-acetylglucosaminidase (NAG)] in hepatic tissue of rainbow trout, Oncorhynchus mykiss (Walbaum) following anti-Y. ruckeri vaccination in the first, second, and sixth months. A concentrated vaccine with Y. ruckeri strains was enclosed in fish feed and was administered three times every other day. Rainbow trout from each group were euthanized 31, 61, and 181 days following vaccination, and hepatic tissue was sampled for analysis. In the current study, vaccination against Y. ruckeri resulted in a no statistically significant change in TBARS levels, while aldehydic and ketonic derivatives of OMP in hepatic tissue decreased, especially after the first and second months following immunization. Moreover, the activities of glutathione-dependent enzymes increased, especially after the first and sixth months. The highest TAC levels were observed two and six months after vaccination. It has been shown that vaccination-related oxidative stress in hepatic tissue is involved in adaptive responses through the temporary mobilization of antioxidant and lysosomal enzymes in rainbow trout. The present study showed the effect of vaccination on lysosome membrane permeability for carbohydrate cleavage after the development of immunity against Yersinia, whereas antioxidant defence was reduced. Our results confirmed that the concept of preserving antioxidant enzyme function after vaccination was also evident when CAT, GR, and GPx activities either increased or were unchanged following vaccination.