The comparative efficacy of silicon (Si) and zinc (Zn) nanoparticles (NPs) in mitigating drought stress in fennel (Foeniculum vulgare) remains largely unexplored. This study evaluated the impact of Si NPs and Zn NPs on enhancing plant growth and physiological-biochemical attributes of fennel under varying irrigation regimes. The 2-year study was a split-pot design with irrigation at three irrigation levels (100, 75, and 50% field capacity, FC) and five treatments of foliar application of Si and Zn NPs (control, 1 mM Si NP, 2 mM Si NP, 1 mM Zn NP, 2 mM Zn NP). Results showed that drought stress reduced plant performance. Increases in superoxide dismutase (SOD, 131%) and catalase (CAT, 276%) were seen after a 50% FC drought without the use of Si and Zn NPs. Conversely, biological yield (34%), seed yield (44%), chlorophyll a + b (26%), relative water content (RWC, 21%), and essential oil (EO) yield (50%) were all reduced. However, application of Zn and Si, particularly 1 mM Si and 2 mM Zn, greatly mitigated drought stress via lowering CAT and SOD activity and enhancing plant yield, chlorophyll content, RWC, and EO. The composition of the EO consisted primarily of anethole, followed by limonene, fenchone, and estragole. During drought conditions, monoterpene hydrocarbons increased while oxygenated monoterpenes decreased. The opposite trend was observed for Si and Zn NPs. Our results suggest that applying Zn NPs at 2 mM followed by Si NPs at 1 mM improved plant resilience and EO yield in fennel plants under water stress.