Previous research showed that pharynx in adult patients with unrepaired isolated cleft palate (UICP) significantly enlarged. However, the literature lacks studies in juvenile patients. Thus, this study aimed to conduct a 3-dimensional evaluation of pharynx in juvenile patients with UICP using cone beam computed tomography. Cone beam computed tomography images of 58 nonsyndromic patients with UICP and 60 noncleft controls aged from 4 to 13 years were acquired. Both patients and controls were divided into 3 groups according to their ages. Image processing and analyses were performed using Mimics and ZWCAD. Linear, angular, planar, and volumetric measurements and comparisons were made. Statistical analyses comparing patients with controls were performed using independent-samples t test, with the threshold of significance set at P = 0.05. Results showed that, in all age groups, anterior height (P = 0.002, P = 0.004, P = 0.004) and length of the floor (P = 0.023, P = 0.000, P = 0.024) of bony nasopharynx; transverse (P = 0.028, P = 0.031, P = 0.043) and posteroanterior (P = 0.000, P = 0.000, P = 0.000) diameters of pharyngeal airway at palatal plane; cross-sectional area of pharyngeal airway at palatal plane (P = 0.006, P = 0.001, P = 0.001); total volume (P = 0.005, P = 0.003, P = 0.038), volume above palatal plane (P = 0.001, P = 0.000, P = 0.005), and volume between palatal plane and C2 plane (P = 0.047, P = 0.025, P = 0.048) were larger in UICP patients. Based on this study, the authors can conclude that pharynx in juvenile UICP patients around the palatal plane was significantly enlarged, and narrowing of velopharyngeal orifice in palatoplasty was seemed important.