This paper presents the design and analysis of a micro-transformer model aimed at achieving high efficiency in photovoltaic applications. The proposed micro-transformer structure consists of two circular planar coils made of copper mounted on PCB (FR4) and Si substrates. The Mohan formula is employed to calculate the micro-transformer’s geometric parameters, ensuring alignment with flyback converter specifications. Consequently, the inductance, quality factors, and coupling factor variation parameters versus frequency, and the impact of the gap between the coils (500, 750, and 1000 µm) on them were analyzed. The simulation findings unequivocally demonstrated that a judicious reduction in gap thickness to 500 µm resulted in a remarkable enhancement of the coupling factor by an impressive 91%. Moreover, finite element-based software was used to analyze the thermal, magnetic, and electric performance of the micro-transformer across varying gap sizes. The investigation led to the determination of the optimal gap thickness that achieves adequate temperature, current, and magnetic flux distribution in the micro-transformer. Finally, the simulation circuit of a photovoltaic system that incorporates a flyback converter including the proposed micro-transformer was performed. Overall, the results revealed that the proposed micro-transformer model with its circular planar coil design offers high efficiency in PV applications.