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In this paper, a procedure for optimal transformer design with a variable set of constraints for pulse transformers with a pulse range of 3-140 μs is presented. During the optimization procedure, the pulse shape is analyzed in the time domain, ensuring that the pulse constraints, such as rise time and overshoot are met. For accurate prediction of the pulse shape, analytical approaches are proposed to estimate the distributed capacitance and leakage inductance of the transformer. The analytical approach is verified by 2-D-FEM simulations and measurements. The optimization procedure considers pulse, core, winding, demagnetization losses, and losses of the primary switches. First, the procedure is applied to an existing pulse transformer with specifications for SwissFEL. An improvement of 16.6% in conversion efficiency is achieved in comparison with the existing design. In a second step, the procedure is applied to specifications of the compact linear collider, which demands high conversion efficiency. The resulting optimal transformer consists of three cores with five primary turns and requires a tank volume of 0.915 m3. In an optimal configuration, an overall conversion efficiency of 97.7% is achieved for the considered system including pulse losses.