A Wilsonian renormalization group (WRG) equation for nuclear currentoperators in two-nucleon systems is derived. Nuclear current operators relevantto low-energy Gamow-Teller transitions are analyzed using the WRG equation. Weemploy the axial two-body current operators from phenomenological models andheavy-baryon chiral perturbation theory, which are quite different from oneanother in describing small scale physics. After reducing the model space ofthe operators using the WRG equation, we find that there still remains asignificant model dependence at \Lambda = 200 MeV, where \Lambda is the sharpcutoff specifying the size of the model space. A model independent effectivecurrent operator is found at a rather small cutoff value, \Lambda = 70 MeV. Bysimulating the effective current operator at \Lambda=70 MeV, we obtain acurrent operator based on a pionless theory, thereby arguing an equivalencerelation between nuclear current operators of phenomenological models and thoseof effective field theories.