The nasopharynx is an important anatomical structure involved in respiration. Its bony boundaries, including the basicranium and upper cervical vertebrae, may be subject to selective pressures and constraints related to respiratory function. Here, we investigate phenotypic integration, or covariation, between the face, the basicranial boundaries of the nasopharynx, and the atlas and axis to understand constraints affecting these structures. We collected three‐dimensional coordinate data from a sample of 80 humans and 44 chimpanzees, and used two‐block partial least squares to assess RV (a multivariate generalization of Pearson's r2), rPLS, the covariance ratio, and effect size for integration among structures. We find that integration is significant among some of these structures, and that integration between the basicranial nasopharynx and vertebrae and between the face and vertebrae is likely independent. We also find divergences in the pattern of integration between humans and chimpanzees suggesting greater constraints among the human face and nasopharynx, which we suggest are linked to divergent developmental trajectories in the two taxa. Evolutionary changes in human basicranial anatomy, coupled with human‐like developmental trajectories, may have required that the face grow to compensate any variation in nasopharyngeal structure. However, we were unable to determine whether the nasopharynx or the face is more strongly integrated with the vertebrae, and therefore whether respiration or biomechanical considerations related to positional behavior may be more strongly tied to vertebral evolution. Future work should focus on greater sample sizes, soft tissue structures, and more diverse taxa to further clarify these findings.