In most primary science classes, students are taught science skills by way of learning by doing. Research shows that explicit instruction may be more effective. The aim of this study is to investigate the effects of explicit instruction in an inquiry-based learning setting on the acquisition of science skills for students in primary education. Participants included 705 Dutch 5th and 6th graders. Students were randomly assigned to either an explicit instruction condition including an 8-week intervention of explicit instruction on inquiry skills; an implicit condition in which students were taught by learning by doing; or a baseline condition in which students followed their regular science curriculum. To assess the effects, measurement instruments for evaluating the acquisition of science skills were developed. Results of a multi-level analysis indicated that explicit instruction facilitates development of science skills. Therefore, this study provides a strong argument for including an explicit teaching method for developing science skills in primary science education.