The objective of this manuscript was to demonstrate the efficacy of silicon supplementation in relieving the fluoride-induced damages in rice cultivar, Khitish. The exposure of seedlings to two different concentrations of fluoride, viz., 25 and 50 mg L−1 NaF caused increase in fluoride accumulation, as a result of which the seedlings suffered severe oxidative stress, as evident from growth inhibition, reduction in seed germination, tissue biomass, root and shoot length, decline in chlorophyll content, increases in electrolyte leakage, H2O2 content, lipid peroxidation (malondialdehyde content and lipoxygenase activity), protein carbonylation and protease activity. The extent of damage was more at higher fluoride concentration. Silicon amendment, irrespective of fluoride concentrations, led to large build-up of endogenous silicon level and brought considerable improvement in all the parameters examined with respect to fluoride stress. The fluoride-mediated enhancement in methylglyoxal level was lowered by silicon, because of the prominent activation of glyoxalase I and glyoxalase II. While the stress-mediated induction in antioxidative enzymes like GPOX, APX, SOD, GPX and GR was lowered by silicon, the inhibition in CAT activity was relieved. The antioxidative defense mechanism was also boosted up via enhanced content of total phenolics and carotenoids. However, the fluoride-mediated increase in anthocyanins, flavonoids, xanthophyll, ascorbate and reduced glutathione, and osmolytes like total amino acids, proline and glycine-betaine, were all lowered in presence of silicon, together with reduced PAL and P5CS activity. Overall, silicon reduced oxidative damages to develop fluoride-tolerant rice plants through augmentation of different antioxidant and osmolyte defense and methylglyoxal detoxification system.