Analysis of salivary volatile organic compounds (VOCs) may offer a novel noninvasive modality for disease detection. This study aims to optimise saliva headspace VOC analysis and assess longitudinal variation of salivary VOCs. Whole saliva from healthy participants was acquired in order to assess four methodological parameters: saliva collection, volume, dilution, and acidification. Saliva VOCs were analysed using untargeted proton transfer reaction time-of-flight mass spectrometry. Using the optimised method, five saliva samples collected over 3 weeks assessed the longitudinal VOC variability and reproducibility with targeted selected ion flow tube-mass spectrometry analysis. The method of saliva collection influenced VOC detection and was a source of contamination. An amount of 500 µL of whole saliva by passive drool yielded optimal VOCs. Longitudinal variation was negligible with target short chain fatty acids and aldehydes. However, certain compounds showed variability suggesting the influence of potential exogenous factors. Overall, there was an acceptable range of inter- and intraindividual VOC variability. Standardisation with morning sampling after a 6 h fast is recommended demonstrating minimal intersubject variability. Future studies should seek to establish salivary VOC levels in healthy and diseased populations.