Persistent fatigue is common among military service members returning from deployment, especially those with a history of mild traumatic brain injury (mTBI). The purpose of this study was to characterize fatigue following deployment, using a multidimensional self-report instrument, the Multidimensional Fatigue Inventory (MFI). The study was developed to test the hypothesis that if fatigue involves disrupted effort/reward processing, this should manifest as altered basal ganglia functional connectivity (FC) as observed in other amotivational states. A finding of effort/reward mismatch may guide future treatment approaches. Twenty-eight current and former service members were recruited and completed the MFI. All twenty-eight has a history of at least one mTBI during deployment. Twenty-six underwent RS fMRI. To test the hypothesis that fatigue was associated with basal ganglia FC, we measured correlations between MFI subscale scores and the FC of left and right caudate, putamen and globus pallidus with the rest of the brain, adjusting for the presence of depression. We found a significant correlation between FC of left putamen and bilateral superior frontal gyri and MF scores. No correlations with the other MFI subscales survived multiple comparisons correction. This exploratory study suggests that mental fatigue in military members with a history of deployment with at least one mTBI may be related to increased striatal-prefrontal functional connectivity, independent of depression.