We investigated the effect of rough surface on the performance of extinction-based localized surface plasmon resonance (LSPR) biosensors. The sensor measures resonance wavelength shifts in transmittance due to biomolecular interactions amplified by periodic nanostructures. The numerical calculation was conducted using rigorous coupled-wave analysis with Gaussian random profiles. The results suggest that, when a surface has a roughness smaller than 2 nm, the sensitivity of an LSPR biosensor is not significantly affected regardless of correlation length (CL). However, we found that extinction peak amplitude and curve width are affected substantially with a decrease in CL. At CL less than 100 nm, surface roughness may induce interference between localized surface plasmons excited by the surface and nanowires, which can lead to significant degradation of sensor performance.