Purpose The purpose of this study is to examine intrafraction variation and residual error (IFV+RE) during conebeam CT (CBCT)-guided hypofractionated prostate radiotherapy and evaluate factors associated along with target margins. Materials and methods Forty-six patients underwent hypofractionated prostate radiotherapy receiving 64 Gy in 20 fractions with on-line CBCT correction. Analysis of factors associated with IFV+RE including patient characteristics, treatment characteristics, and organ volumes was performed using univariate and multivariate analyses. Results The mean IFV+RE were 0.10±1.1, −1.1±2.5, and −1.5 ±2.7 mm in the mediolateral (ML), anteroposterior (AP), and craniocaudad (CC) dimensions, respectively. The IFV+RE vector was 3.5±2.5 mm. It was found that 1, 22, and 31 % of fractions had an IFV+RE greater than 3 mm in the ML, AP, and CC dimensions, respectively. Multivariate analysis found that age and rectal volumes are associated with increased IFV+RE. When evaluating IFV+RE greater than 3 mm, age, treatment time, and rectal volumes were associated. A treatment time of greater than 16.5 min was found to be a cut point for increased IFV+RE. Conclusions IFV may represent a significant component of target margins utilized in hypofractionated prostate radiotherapy with target margins exceeding 3 mm in the CC and AP dimensions. Rectal volumes, treatment time, and age are associated with IFV+RE.