Three-phase dual active bridge converters (DAB3) are a widely used topology in battery charging applications thanks to their numerous advantages, such as bidirectional power flow, galvanic isolation, low output current ripple, and inherent soft-switching. In such applications, three single-phase transformers are commonly employed as the AC-link to simplify manufacturing and reduce costs. These transformers’ leakage inductance can be utilized instead of the external leakage inductance to achieve high power density. However, the assumption of uniformity in these inductances is not always accurate as they can vary significantly during fabrication. This study presents a comprehensive analysis of the impact of transformer leakage inductance variation, which can deviate by up to 24% from the desired value. The effects of this variation are investigated from different perspectives, including power transfer, soft-switching range, root-mean-square (RMS) current, and the temperature rise of the transformer winding. Although the power transfer and total copper loss of transformers are changed insignificantly even under highly mismatched leakage inductance, the currents and thermal distribution among phases are considerably impacted. Based on statistical probability, a maximum leakage inductance variation threshold of 10–15% compared to the desired value is recommended to ensure the maximum acceptable temperature rise among phases. Experimental results are presented to validate the analysis.