The interaction between the fully reduced flavin-adenine dinucleotide (FADH(-)) and thymine dimer (T)(2) has been investigated by means of density functional theory (DFT) calculations. The charges of FADH(-) and (T)(2) were calculated to be -0.9 and -0.1, respectively, at the ground state. By photoirradiation, an electron transfer occurred from FADH(-) to (T)(2) at the first excited state. Next, the reaction dynamics of electron capture of (T)(2) have been investigated by means of the direct ab initio molecular dynamics (MD) method (HF/3-21G(d) and B3LYP/6-31G(d) levels) in order to elucidate the mechanism of the repair process of thymine dimer caused by the photoenzyme. The thymine dimer has two C-C single bonds between thymine rings (C-5-C-5' and C-6-C-6' bonds) at the neutral state, which is expressed by (T)(2). After the electron capture of (T)(2), the C-5-C-5' bond was gradually elongated and then it was preferentially broken. The time scale of the C-C bond breaking and formation of the intermediate with a single bond (T)(2)(-) was estimated to be 100-150 fs. The present calculations confirmed that the repair reaction of thymine dimer takes place efficiently via an electron-transfer process from the FADH(-) enzyme.