Dental cone beam computed tomography (CBCT) is a diverse 3D X-ray imaging technique that has enabled clear visualization of the teeth and surrounding structures. The most common diagnostic purpose of dental CBCT examination in children is ectopic eruption and impacted teeth, and a small field of view (FOV) is often used. Since it is difficult for children to control their body movements, reducing the rotation angle is effective. However, no studies have examined the effects of different rotation angles on radiation doses to highly radiosensitive organs in children using small FOVs. The purpose of this study was to examine the effects of small FOVs (4 × 4 cm and 6 × 6 cm) and rotation angles (360° and 180°) on doses that highly sensitize organs in children using dental CBCT. The entrance surface doses to lenses, thyroid lobes, parotid glands, and sublingual glands of a pediatric whole-body phantom were measured. By reducing the FOV from 6 × 6 cm to 4 × 4 cm, the dose to the sublingual gland could be significantly decreased. Additionally, by reducing the rotation angle from 360° to 180°, the lens dose can be decreased significantly. As the rate of dose reduction varies among organs, it is important to consider the relative positions of different organs with respect to the FOV and the trajectory of the X-ray tube.