This study used kilovoltage (kV) cone beam computed tomography (CBCT) imaging to characterize canine intrafractional prostate motion during hypofractionated stereotactic radiotherapy treatment. Serial CBCT images taken just prior to initiating treatment, and at several times during the treatment session, were acquired throughout the course of treatment for canine patients. All patients were immobilized in dorsal recumbency while using an air-inflated rectal balloon. For each treatment session, rigid registration of intrafraction CBCT images with the interfraction CBCT used for setup verification was performed. Contours of the prostate and urethra were drawn on each CBCT image set and the center of mass for each structure was evaluated as a function of time. A total of seven canine patients was included in the study, resulting in 41 CBCT images collected during a total of 12 treatment sessions. Over 70% of our data were collected for CBCTs taken between 20 and 51 min after final patient setup was complete. The mean intrafraction movement in a single direction for the prostate and urethra was ≤0.14 mm and ≤0.22 mm, respectively. The maximum intrafraction movement for the prostate and urethra was ≤ 1.60 mm and ≤ 2.00 mm, respectively. The maximum variability in intrafraction movement for the prostate and urethra, as defined by two standard deviations, was ≤1.40 mm and ≤1.50 mm, respectively. Minimal intrafraction variability using appropriate patient positioning and rectal balloon, combined with kV CBCT image-guided radiation therapy tools to account for interfraction changes, permit accurate and precise targeting of structures of interest.