The development of the transport plan must take into account various criteria impacting the transport process. The main objective of the study is to propose an integrated approach to determine the transport plan of passenger trains. The methodology consists of five steps. In the first step, the criteria for optimization of the transport plan were defined. In the second step, variants of the transport plan were formulated. In the third step, the weights of the criteria are determined by applying the step-wise weight assessment ratio analysis method (SWARA) multi-criteria method. The multi-objective optimization was conducted in the fourth step. The following multi-objective optimization approaches were used and compared: weighted sum method (WSM), compromise programming method (CP), and the epsilon–constraint method (EC). The study proposes a modified epsilon–constraint method (MEC) by applying normalization of each objective function according to the maximal value of the solution by individual optimization for each objective function, and hybrid methods: hybrid WSM and EC, hybrid WSM and MEC, hybrid CP and EC, and Hybrid CP and MEC. The impact of the variation of passenger flows on the choice of an optimal transport plan was studied in the fifth step. The Laplace’s criterion, Hurwitz’s criterion, and Savage’s criterion were applied to come to a decision. The approbation of the methodology was demonstrated through the case study of Bulgaria’s railway network. Suitable variant of transport plan is proposed.