Background: This study aimed to compare the therapeutic outcomes and fatal carotid blow out syndrome (CBOS) incidence rates between two different stereotactic body radiotherapy (SBRT) protocols. Methods: The study included 75 patients with inoperable locally recurrent head and neck cancer treated with SBRT in our department between June 2007 and March 2011. The first 43 patients were treated sequentially (group I). Then our SBRT protocol was changed due to the high rate of CBOS, and the following 32 patients were treated every other day in a prospective institutional protocol (group II). Results: Median overall survival in group I and group II was 11 months and 23 months, respectively (P = 0.006). We observed 11 cases of CBOS. Only 1 of 7 patients (14%) with CBOS survived in group I, whereas 2 of 4 patients (50%) in group II remain alive. CBOS free median overall survivals were 9 months, and 23 months in group I and group II respectively (P = 0.002). The median radiation dose received by the carotid artery in patients with CBOS was 36.5 Gy (range: 34–42.8 Gy), versus 34.7 Gy (range: 0–44 Gy) in the patients that didn’t have CBOS (P = 0.15). CBOS did not occur in any of the patients with a maximum carotid artery radiation dose <34 Gy. Conclusions: Every other day SBRT protocol for re-irradiation of recurrent head and neck cancer is promising in terms of decreasing the incidence of fatal CBOS.