The purpose of the article is to evaluate the effectiveness of the Management by Objectives (MBO) system applied at a higher education institution, specifically at the Institute of Technology and Business in České Budějovice. Generally, effectiveness can be defined as a favourable ratio of inputs and outputs where we are able to measure only the least ineffective value of the attained outputs using a specific number of inputs (however, not the point of absolute effectiveness). For the collection of data we used a management and control system called Excellent Top Manager System (ETMS) which was originally developed as a tool for the registration of the performance of employees working at the Institute of Technology and Business (ITB) in České Budějovice. The ETMS is used at the Institute for the provision of planning, supervising and follow-up evaluation of the fulfilment of objectives set by individual sections, departments as well as by individual employees of the Institute. Considering the quantity of data and the scope of the subject, the article focuses specifically on the effectiveness of the management of teaching, research and other creative activities performed at the Institute of Technology and Business in České Budějovice.