Previous research of inquiry-based learning in natural science education indicates that there are different methodological trends and paradigms in the study of these issues. The aim of this research has been to analyze the selected relevant studies on inquiry-based learning in natural science education in order to assess their scope and limitations in the light of educational changes and reform initiatives. Directions of analysis of the relevant studies include considerations of the following: 1) Theoretical starting points and specific conceptual solutions, 2) Methodological design (research questions / problems, methods, techniques, and procedures), as well as 3) (Re)interpretation of the most significant findings. It could be stated that studies on inquiry-based learning in the field of natural sciences are rather insufficient, very diverse and heterogeneous, differing from each other both in terms of theory and conceptual solutions, research problems, methodological design, and implications for educational work. Even though experiments are very common in natural sciences, it has been found that triangulation is often used as a combination of qualitative and quantitative paradigms. The common thread that connects the selected studies in this field is the recognition of importance of inquiry-based learning as a very promising model of active teaching the natural sciences. It could be concluded that such studies require an interdisciplinary approach to the subject of study, both in empirical and theoretical field, providing better understanding of the future research directions of this phenomenon.