Background: Nasal septum deviation (NSD) can cause serious anatomical and clinical complications. It can change the breathing pattern and thus alter the anatomy of the airway structures. Despite its importance, the association between NSD with the nasopharynx volume (NPV) has not been assessed before. Therefore, we aimed to investigate it for the first time. Methods: Archival CBCTs of 202 patients older than 17 years and without any history of trauma or pathology of the nasopharynx and without any orthodontic/orthognathic treatments were evaluated (129 women, 73 men, mean age: 36.24 ± 14.61 years). All included CBCTs must have been taken with a 12 × 8 field of view and fully covered the nasopharynx areas. The extent of NSD (°) and NPV (mm3) were measured. NSDs were categorized as mild (NSD ˂ 9°), moderate (9 ≤ NSD ≤ 15°), and severe (NSD ˃ 15°). Associations between sex, age, NSD, and nasopharynx volume were assessed using independent-samples t test, chi-square, one-way ANOVA, Tamhane post hoc test, Pearson and point-biserial correlation coefficients, and multiple linear regressions (α = 0.05). Results: Mean NSDs were 11.27 ± 4.69° (range 1–19.5), 11.58 ± 4.63°, and 10.70 ± 4.76° in the sample, females, and males, respectively (P > 0.05). Of females, 27.9%, 40.3%, and 31.8% had mild, moderate, and severe NSDs. These were 35.6%, 39.7%, and 24.7% in males (P > 0.05). Mean NPVs were 4.88 ± 1.49, 4.80 ± 1.43, and 5.04 ± 1.60 mm3 in the sample, females, and males, respectively (P > 0.05). Mean NPVs were 6.41 ± 1.21, 4.87 ± 0.73, and 3.30 ± 0.65 mm3 in mild, moderate, and severe NSD groups (all P values = 0.000). Mean ages were 27.06 ± 6.49, 29.80 ± 9.64, and 54.73 ± 8.45 years in mild, moderate, and severe NSD groups (severe group being older than the other two groups, P = 0.000). NSD was strongly, negatively correlated with NPV (R = − 0.793, P = 0.000). Sex was not correlated with NPV or NSD (P ≥ 0.189). Age was negatively and positively correlated with NPV and NSD, respectively (P = 0.000). Modeling NSD (β = −0.776, P = 0.000) as a predictor for NPV rendered age effect insignificant (P > 0.05). Conclusions It was found, for the first time, that the more deviated the nasal septum, the smaller the nasopharynx volume. Aging might increase NSD and through it, reduce the nasopharynx volume. Sex might not affect NSD or NPV.