In this paper, a conventional 12-pulse transformer unit (CTU) and an autotransformer 12-pulse transformer unit (ATU) are compared in the view of the RTCA DO-160 standard for aircraft applications. The design of the magnetic components is proposed via a coupled FEM-circuital analysis in the time domain for an 800 Hz/2 kW system. Input AC distortion, power factor, and output DC ripple are evaluated through simulations. An accurate power loss analysis is carried out, taking into account copper losses, magnetic losses, and power losses due to power switches. The reduction in the size and weight of the ATU with respect to the CTU solution is discussed, including the need for filtering systems and the standard requirements.