Reducing the distance between the fluorescence molecules and noble metal (resonant) nanostructures is known to advance the process of electromagnetic coupling and energy transfer, which in return yields fluorescence enhancement particularly exploited for improved biomedical applications. In this study, Au-capped Si nanowhiskers (NWs) at various sizes were fabricated using a vapor-liquid-solid (VLS) mechanism for systematically investigating the dependence of the size of the Au-capped Si NWs on the fluorescence enhancement factor with respect to the fluorescence emission from Rhodamine 6G (Rh-6G) fluorophore. Opposite to what is anticipated from the literature, the maximum enhancement was obtained for the sample for which the Au-nanoparticle (NP) capping is well isolated from the fluorophore and the vertical distance between the fluorophore and the plasmonic metal nanoparticle is largest. Numerical simulations using the finite element method (FEM) were shown to support the experimental optical response results. Four-point probe I-V measurements also show that the Schottky ideality factor of Au-capped Si NWs decays exponentially upon the rise in the fluorescence enhancement factor.