Traumatic brain injury (TBI) as a major public health problem may lead to olfactory dysfunction. However, little is known about brain responses to odors in TBI olfactory loss patients. Nineteen healthy controls and forty TBI olfactory dysfunctional patients (19 with hyposmia and 21 with anosmia) underwent a functional magnetic resonance imaging scan when two odors (peach and coffee) were presented intranasally using a computerized olfactometer. Olfactory performance was measured using the “Sniffin’ Sticks” test. TBI patients with hyposmia or anosmia showed decreased odor-induced brain activations in the primary olfactory area and insular cortex as compared to healthy controls (FWE-corrected peak p < 0.05). In addition, negative correlations were found between the time since injury (in month) and odor-induced brain responses in the right primary olfactory area for patients with hyposmia. Similar correlations were seen in the insula and orbitofrontal cortex for patients with anosmia. In conclusion, results from the current study are evidences for the impairment of central nervous processing of odor perception at all levels of the olfactory system among TBI patients with olfactory loss. In addition, the duration after the initial injury may have an impact on the severity of olfactory dysfunction.