Approximated functional renormalization group (FRG) equations lead to regulator-dependent beta-functions, in analogy to the scheme-dependence of the perturbative renormalization group (pRG) approach. A scheme transformation redefines the couplings to relate the beta-functions of the FRG method with an arbitrary regulator function to the pRG ones obtained in a given scheme. Here, we consider a periodic sine-Gordon scalar field theory in d=2 dimensions and show that the relation of the FRG and pRG approaches is intricate. Although, both the FRG and the pRG methods are known to be sufficient to obtain the critical frequency of the model independently of the choice of the regulator and the renormalization scheme, we show that one has to go beyond the standard pRG method (e.g., using an auxiliary mass term) or the Coulomb-gas representation in order to obtain the beta-function of the wave function renormalization. This aspect makes the scheme transformation non-trivial. Comparing flow equations of the two-dimensional sine-Gordon theory without any scheme-transformation, i.e., redefinition of couplings, we find that the auxiliary mass pRG beta-functions of the minimal subtraction scheme can be recovered within the FRG approach with the choice of the power-law regulator with b=2, therefore constitutes a preferred choice for the comparison of FRG and pRG flows.