The article is devoted to the automation of the process of planning and management of operational activities in a multidisciplinary hospital – the basic principles and features, parameters and factors affecting the formation of the operation plan are formulated, the model of the business process is described and criteria for its effectiveness are given, the methodological foundations for organizing the planning of operational activities are shown – shown the leading role of the relationship between the plan of operations and the plan of hospitalizations, the role of the medical information system in the automation of operational activities is determined. All identified methods of increasing the efficiency of the operational activity of medical institutions by means of MIS were tested on the example of using MIS Interin PROMIS Alpha at the Federal Research and Clinical Center of the FMBA of Russia. The results that were achieved as a result of the practical application of these methods with the use of MIS in the organization of the daily process of the activities of surgeons in the Federal Research Center of the Federal Medical and Biological Agency of the Federal Medical and Biological Agency of Russia are considered.