Background The purpose of this study was to examine whether the temperature difference between the jugular bulb and pulmonary artery (ΔT_jb-pa) is associated with the neurological outcome of patients with severe traumatic brain injury (TBI). Methods We conducted a post hoc analysis of a multicenter randomized controlled trial of mild therapeutic hypothermia (TH, 32.0–34.0°C) or fever control (FC, 35.5–37.0°C) for the patients with severe TBI. ΔT_jb-pa averaged every 12 h and the variation in ΔT_jb-pa were compared between patients with favorable (n = 39) and unfavorable (n = 37) neurological outcomes. These values were also compared in the TH and FC subgroups. Results The average ΔT_jb-pa values in patients with favorable and unfavorable outcomes were 0.24 ± 0.23 and 0.06 ± 0.36°C, respectively (P < 0.001). ΔT_jb-pa trended significantly higher in the favorable outcome patients than in the unfavorable outcome patients throughout the 120 h after onset of severe TBI (P < 0.001). The variation in ΔT_jb-pa from 0 to 72 h was significantly lower in the favorable outcome patients than in the unfavorable outcome patients (0.8 ± 0.8 vs 1.8 ± 2.5°C, respectively, P = 0.013). From 72 to 120 h, there was no significant difference in the variation in ΔT_jb-pa. Significant differences between patients with favorable and unfavorable outcomes in ΔT_jb-pa and the variation in ΔT_jb-pa were similar in the TH subgroup, but not evident in the FC subgroup. Conclusions A reduction in ΔT_jb-pa and greater variation in ΔT_jb-pa were associated with an unfavorable outcome in patients with severe TBI, especially those treated with TH. When treating severe TBI patients, it is important to understand that there will be differences in temperature reflecting the brain environment and the systemic temperature, depending on the severity and outcome of TBI during TH.