A highly sensitive and specific detection of 2,4,6-trinitrotoluene (TNT), a typical nitrated aromatic explosive, was demonstrated by a silicon nanowire (SiNW) array sensor. The SiNW array devices were self-assembled and functionalized with the anti-TNT peptide to obtain unique sensitivity toward TNT. Also, the effect of the biointerfacing linker's chemistry and Debye screening with varied ionic strength of phosphate buffer solution (PBS) on TNT binding response signals were investigated. The optimization of the peptide-functionalized SiNW array sensor showed high sensitivity for TNT with a detection limit of 0.2 fM, the highest sensitivity reported to date. These initial promising results may help accelerate the development of portable sensors for femtomolar level TNT detection.