Teachers can develop science literacy among pupils through Inquiry-Based Science Education. IBSE helps to evolve the inquiry skills necessary for understanding the world of science and nature. To be able to improve the level of inquiry skills systematically, we need to know the current level among pupils. For this reason, we designed a multiple-choice test that measures the level of inquiry skills among 13 to 15 years old pupils. The design of the test consisted of six steps: selection of inquiry skills, construction and administration of open-ended test, creation of a database of distractors, construction of multiple-choice test, pilot testing and application of optimised test in pedagogical research. The designed test can be considered a valid and reliable research instrument and the individual test items show a relatively high discriminating power, optimal level of difficulty and a high number of functional distractors. By analysing the most common incorrect answers, we were able to identify various difficulties pupils have, regarding the application of inquiry skills in solving items. These results will help us to design appropriate strategies for improving pupils' inquiry skills in science education.