The aims of this study were (1) to quantify the intra-individual variation in the upper airway measurements on supine computed tomography (CT) scans at two different time points; and (2) to identify the most stable parameters of the upper airway measurements over time. Ten subjects with paired CT datasets (3–6 months interval) were studied, using computer software to segment and measure the upper airway. The minimum cross-sectional area of the total airway and all its segments (velopharynx, oropharynx, tongue base, and epiglottis) generally had the largest variation, while the length of the total airway had the lowest variation. Sphericity was the only parameter that was stable over time (relative difference <15%), both in the total airway and each subregion. There was considerable intra-individual variation in CT measurements of the upper airway, with the same patient instruction protocol for image acquisitions. The length of the total airway, and the sphericity of the total upper airway and each segment were stable over time. Hence, such intra-individual variation should be taken into account when interpreting and comparing upper airway evaluation parameters on CT in order to quantify treatment results or disease progress.