PEGylated graphene oxide nanoparticle (PEG-nGO) has been commonly used as a carrier for therapeutic drugs and vaccines, because of its unique properties, such as high solubility, more stability and increased biocompatibility in physiological solutions. This study aimed to examine the DNA damage and neurotoxicity in young mice after up to 4 h of the treatment with PEG-nGO. A single dose (5 mg/kg) of intravenous injection was administered through the tail vein of adult mice. Total genomic DNA was isolated from the control and treated animals after 1 h, 2 h, and 4 h of treatments and examined for DNA damage by diphenyl assay, DNA fragmentation Assay, and FTIR (Fourier transform infrared) techniques. DNA damage studies indicated DNA fragmentation after 1 h and 2 h of treatments followed by recovery at 4 h. FTIR analysis further supported these results and showed a detailed molecular effect of the treatments that caused single and double-strand DNA breaks at 1 to 2 h after the treatments and indicated DNA damage response and recovery at 4 h. Histopathology showed neuronal apoptosis and lesions in the brain after 1 to 2 h and invasion of inflammatory response and chromatolysis after 4 h. PEG-nGO caused immediate DNA damage and cytotoxicity to the brain and its future use as a drug carrier should be considered with caution.