To achieve high power-density isolated dc-dc converter, gallium nitride high electron mobility transistors (GaN-HEMTs) and planar transformer have been used. Also, for the high power-density design, these components are placed close to each other. GaN-HEMTs are significantly affected by the leakage flux of the planar transformer, because of their lateral structure. Therefore, the mutual effects of the components are needed to take into account. This paper presents the leakage flux effects of the planar transformer on GaN-HEMTs in 5 MHz isolated dc-dc converter. Moreover, to suppress the effects, the method using the magnetic shield as the part of the printed circuit board (PCB) layout has been proposed. The effects and the proposed method have been analyzed by finite element method (FEM) with Maxwell 3D. Some experiments have been done with 5 MHz unregulated LLC resonant dc-dc converter with GaN-HEMTs; the input voltage is 48 V, the output voltage is 12 V, and the size is 17 mm × 25 mm × 6.5 mm. From the experimental results, by inserting the magnetic shield, the load current range is improved from 6 to 8 A. In addition, the maximum temperature is improved 17.1 °C, and the power efficiency is increased 1.58 % at 6 A.