We investigated differences in brain activation associated with cognitive fatigue between persons with traumatic brain injury (TBI) and healthy controls (HCs). Twenty-two participants with moderate-severe TBI and 20 HCs performed four blocks of a difficult working memory task and four blocks of a control task during fMRI imaging. Cognitive fatigue, assessed before and after each block, was used as a covariate to assess fatigue-related brain activation. The TBI group reported more fatigue than the HCs, though their performance was comparable. Regarding brain activation, the TBI group showed a Task X Fatigue interaction in the caudate tail resulting from a positive correlation between fatigue and brain activation for the difficult task and a negative relationship for the control task. The HC group showed the same Task X Fatigue interaction in the caudate head. Because we had prior hypotheses about the caudate, we performed a confirmatory analysis of a separate dataset in which the same subjects performed a processing speed task. A relationship between Fatigue and brain activation was evident in the caudate for this task as well. These results underscore the importance of the caudate nucleus in relation to cognitive fatigue.