Heavy ion therapy is becoming widely known and used as an advanced therapy for cancer. However, the effects of heavy ion therapy on healthy neurons surrounding the cancer and on the higher brain function are still poorly understood. To reveal the effects of heavy ion irradiation on the brain, we analyzed the effect of carbon ion beam in vitro and in vivo. We prepared the mouse primary hippocampal cultures, and irradiated them at 21 DIV (days in vitro) with single dose of 10 Gy of Carbon ion beam. Then we fixed those cells at 2 hr, 8 hr, and 24 hr after the irradiation, and stained them with an anti-cleaved Caspase-9 antibody as a marker for cellular damage and an anti-GFAP antibody for astrocytes. Immunofluorescence microscopy showed that cleaved Caspase-9 positive cells were significantly increased after 2 hr following the irradiation. Interestingly, cleaved caspase-9 positive cells were only found on neurons but not on GFAP positive cells at least within 24 hr. We next conducted fear conditioning test using mice to evaluate acute effects of carbon ion beam on higher brain function. Using 10-12 weeks old C57BL/6 male mice, single dose of 10 Gy of Carbon ion beam was administered to their whole brains. We conducted fear conditioning training 7 hr and 24 hr after irradiation. We tested those mice for context test 24 hr after training and for tone test 48 hr after training. We found when mice were irradiated 24 hr before training, mice were not able to retrieve the context but they could perform tone test as well as control. These results indicate that the acute effects of Carbon ion beam on the neuronal cell death process started to appear from 2 hr. The single dose of 10 Gy of Carbon ion beam impaired the hippocampus dependent fear memory formation 24 hr after irradiation.