The brain level of perfluorododecanoic acid (PFDoA) was compared with those of perfluorooctanoic acid (PFOA) and perfluorodecanoic acid (PFDA) in rats 9 days after a single oral dose (50 mg/kg). The PFDoA level in the brain was 44.0 ± 2.0 µg/g, which was higher than that in the serum (24.4 ± 1.0 µg/ml). In contrast, the concentrations of PFOA and PFDA in the brain were low (<0.8 and 4.7 ± 0.4 µg/g, respectively), and less than one-tenth of those in the serum. Next, to investigate the effects on brain function, the cognitive function alterations of PFOA, PFDA, and PFDoA were estimated by the novel object recognition test 5-6 days after dosing. A significant decrease in the discrimination index was observed in PFDoA-treated rats while no significant alteration was observed in PFDA- and PFOA-treated rats. The effects of PFDoA were further assessed by other behavioral tests. PFDoA-associated alteration was observed in the elevated-plus maze test, but not in the Y-maze test, open-field test, and forced swim test. A decrease in the discrimination index of the novel object recognition test was dependent on the PFDoA dose and the PFDoA concentration in the brain. PFDoA concentration in the brain was 28.6 ± 2.6 µg/g 30 days after dosing, and a decrease in discrimination index was observed. Taken together, these results suggest that PFDoA distributes in the brain easier than PFOA and PFDA and causes cognitive deficit.