The transport system is an essential part of Kazakhstan’s economy and a key factor in boosting the country’s competitiveness. Kazakhstan’s unique location, bridging Europe and Asia, gives it a natural advantage in the global economic system. Transport companies are now under pressure to meet strict external demands. One way to address these challenges is by choosing an optimal investment portfolio for transport subsystems. Using the Markowitz model, originally designed for securities, this approach has been adapted to create a balanced portfolio for real investments. This research is important as it solves the complex task of identifying the most optimal choice among a set of potential project portfolios. The core of this challenge lies in achieving a balance across various quality metrics. The research emphasizes creating a method to select the best project portfolio from acceptable alternatives, leveraging a range of optimality criteria worked out by the Markowitz model. The practical significance of the research findings lies in their applicability to real-world strategic decision-making. The theoretical principles developed in this research provide a robust foundation for designing optimal portfolios of investment projects. These portfolios can be tailored to align with the strategic management objectives of various economic sectors, ensuring resource allocation is efficient and aligned with long-term development goals.