A method for the identification of key volatile organic compound (VOC) markers associated with infection by Neisseria meningitidis bacteria by gas chromatography–mass spectrometry (GC–MS) was developed. Headspace samples of bacterial VOCs were trapped on triple-sorbent bed tubes and then thermally desorbed into a laboratory GC–MS system for separation. Identification was carried out by comparison of GC retention time and electron ionization mass spectra to the National Institute of Standards and Technology (NIST) database. Further confirmation was obtained by GC–MS of known standard chemicals. A total of 75 VOCs were detected, five of which can be considered key VOC markers for Neisseria meningitidis. These peaks were identified as 1,2-dimethylcyclopropane, 2-methylpropanal, methacrolein, N-2-dimethyl-1-propanamine, and 3-methylbutanal by the NIST database.