In this study, the effects of probiotic administration on zebrafish Danio rerio intestinal innate immunity and hepatic stress were evaluated. Zebrafish adults were treated for 10 days with the probiotic Lactobacillus rhamnosus IMC 501(®). To assess the effects at the molecular level, the mRNA levels of genes involved in the innate immune system, stress response, oxidative stress, and apoptosis were quantified by real-time polymerase chain reaction. An increase of biomarkers related to innate immune responses was observed in intestinal tissue from the probiotic-treated fish compared with the control fish. In addition, a decrease in the abundance of stress and apoptotic-related genes was observed in the liver of the probiotic-fed fish. Finally, imaging Fourier transform infrared analysis was conducted on liver sections and the data obtained confirmed that probiotic administration decreased oxidative stress levels, decreased DNA damage, and increased lipid saturation levels. Overall, the results show that probiotic administration may enhance zebrafish welfare by modulating the innate immune response and improving hepatic stress tolerance.