The possibility of using a balanced scorecard (BSS) system for assessing the activity of a project-oriented shipping company was explored. The structure of the BSS, which consists of three subsystems, is proposed: the main type of activity, the project activity, the related activity. Each subsystem is formed by a set of indicators, which describe the data of the subsystem. «Main type of activity» and «Project type of activity» are considered in the following directions: the personnel section, the organizational section, the production section, the marketing section and the financial section. «Project activity» consists of the essence of the project, resources, risks, the efficiency, the quality. It was offered to consider the project-oriented shipping company as a system in the dynamics of its development. Proceeding from this, a model of cause-effect relationships between the subsystems of the balanced scorecard system was developed, considering the development objectives of the shipping company at each stage of its life cycle. Five stages are distinguished: birth, becoming, maturity, aging, rebirth or extinction.