This paper explores the occurrence of a Simpson’s paradox in PISA 2015 science literacy data. Simpson’s paradox, a case of contradicting interpretations when results are analysed by groups or aggregated as a whole, has both a practical and an academic significance. It is an interesting phenomenon that is far from theoretical and when it happens, it has profound effects on the interpretation and if left unidentified can cause confusion and misunderstanding. This paper demonstrates best ways to detect Simpson’s paradox through appropriate tables and graphs. Actual occurrences of a Simpson’s paradox and conditions leading to them are explored using PISA 2015 gender differences in science literacy data in five central European countries − Austria, Croatia, Czech Republic, Slovakia and Slovenia. In countries where the occurrence of a Simpson’s paradox was detected, we provide correct interpretation of the results. Beside creating problems with interpretation an occurrence of a Simpson’s paradox also provides new insight − it signifies that there is very different gender composition in different educational tracks which has important implications for the educational governance. We will discuss implications of these findings in context of Slovenian educational system.