International research shows that the concept of academic futility is a promising one for studying the mechanisms that cause differences in educational outcomes in general and vocational secondary school programmes. Given that there are large differences between general and vocational programmes in the Czech education system, in terms of the content of education, the conditions of education, student composition, and learning outcomes, it is important to take a deeper look at the causes of these differences. The aim of this paper is to test the original, three-dimensional version of the concept of academic futility at Czech secondary schools. The concept was tested on data obtained from a sample of 4857 students from 29 grammar schools and 90 secondary technical schools who attended the third year of secondary school in the school year 2018/2019. Confirmatory factor analysis indicated a good model fit with the data for the one-level (student level) and two-level (student and class level) concepts. Measurement invariance was evaluated for different eduational tracks. The potential of using a two-level concept for research on the educational pathways of Czech secondary school students attending various educational programmes is discussed.