Common mode (CM) Electromagnetic interference (EMI) noise in an isolated converter is mainly due to parasitic capacitance occurring within the SMPS (Switch-mode Power Supply). It flows through transformer coupling capacitance and the parasitic capacitance of MOSFETs and diodes. Several techniques have been proposed in the literature to mitigate the common mode noise flowing through transformer windings. Transformer shielding is one of the most effective methods to reduce EMI noise between the primary and secondary windings, however. However, further improvement should be possible by developing more precise models. In this paper, we develop an EMI noise model for an isolated converter that allows detailed performance analysis. It incorporates the parasitic elements of the converter components and also the coupling capacitance of the transformer. Using this model we propose a new balancing technique to mitigate the CM noise of the isolated converter with modified transformer. The proposed method is applied to an isolated converter and experimental results are provided to verify the novel balancing technique.