The current investigation assessed the impacts of sub-lethal concentrations of silicon dioxide nanoparticles (SiO2NPs) on hepato-renal functions, histopathological characteristics, and gene transcription in gills and liver of Nile tilapia juveniles. Fish were exposed to 20, 40, and 100 mg/L of SiO2NPs for 3 weeks. Pairwise comparisons with the control group showed a significant dose-dependent elevation in serum ALP, ALT, and AST enzyme activities as well as blood urea and creatinine levels in SiO2NP-intoxicated groups. Exposure to 100 mg/L SiO2NPs significantly upregulated expression of HSP70, TNF-α, IL-1β, and IL-8 genes in the gills as compared to the control group. Moreover, exposure to 100 mg/L SiO2NPs significantly upregulated the expression SOD, HSP70, IL-1β, IL-8, and TNF-α genes in the hepatic tissues as compared to the control group. Exposure of fish to 20 mg SiO2NPs/L significantly increased the mRNA expression levels of IL-12 in both the gills and liver tissues. Notably, all tested SiO2NP concentrations significantly upregulated the transcription of CASP3 gene in gills and liver of Nile tilapia as compared to the control group. Interestingly, varying histopathological alterations in renal, hepatopancreatic, and branchial tissues were observed to be correlated to the tested SiO2NP concentrations. In conclusion, our results provide additional information on the toxic impacts of SiO2NPs in Nile tilapia at the hematological, tissue, and molecular levels.