<jats:title>Abstract</jats:title><jats:sec><jats:title>Purpose</jats:title><jats:p>With a new tumor‐tracking system (Synchrony®) for tomotherapy (Radixact®), the internal and set‐up margins can be tightened, like cyberknife (CyberKnife®), in the planning of stereotactic body radiotherapy (SBRT) for prostate cancer. Recently, the usefulness of placing a hydrogel spacer between the prostate and rectum has been established in prostate radiotherapy. We evaluated the characteristics of tomotherapy plans with the tumor‐tracking system and compared them with cyberknife SBRT plans for localized prostate cancer using a hydrogel spacer.</jats:p></jats:sec><jats:sec><jats:title>Methods</jats:title><jats:p>In 20 patients, two plans were created and compared using tomotherapy and cyberknife. All patients underwent hydrogel spacer injection behind the prostate before simulation CT and MRI for fusion. For all plans, 36.25 Gy in 7.25‐Gy fractions for a minimum coverage dose of 95% of planning target volume (PTV) (D95%) was prescribed. The D99% of PTV and D0.1 ml of the PTV, urethra, bladder, and rectum were intended to be > 90%, 110–130%, 100–110%, <110%, and <100%, respectively, of the prescribed doses.</jats:p></jats:sec><jats:sec><jats:title>Results</jats:title><jats:p>All plans using tomotherapy and cyberknife achieved the intended dose constraints. The cyberknife plans yielded better median PTV‐V110% (volume of PTV covered by 110% isodose line, 54.8%), maintaining lower median D0.1 ml of the urethra (37.5 Gy) and V80% of the bladder (11.0 ml) compared to the tomotherapy plans (39.0%; <jats:italic>p </jats:italic>< 0.0001, 38.2 Gy; <jats:italic>p</jats:italic> < 0.0001, and 18.3 ml; <jats:italic>p</jats:italic> < 0.0001, respectively). The tomotherapy plans were superior to the cyberknife plans for the rectum (V80% = 0.4 vs. 1.0 ml, <jats:italic>p</jats:italic> < 0.001; D1ml = 26.4 vs. 29.0 Gy, <jats:italic>p</jats:italic> = 0.013).</jats:p></jats:sec><jats:sec><jats:title>Conclusions</jats:title><jats:p>Our results suggested that tomotherapy with the tumor‐tracking system has reasonable potential for SBRT for localized prostate cancer using a hydrogel spacer.</jats:p></jats:sec>