In most primary science classes, students are taught science inquiry skills by way of learning by doing. Research shows that explicit instruction may be more effective. The aim of this study was to investigate the effects of explicit instruction on the acquisition of inquiry skills. Participants included 705 Dutch fifth and sixth graders. Students in an explicit instruction condition received an eight-week intervention of explicit instruction on inquiry skills. In the lessons of the implicit condition, all aspects of explicit instruction were absent. Students in the baseline condition followed their regular science curriculum. In a quasi-experimental pre-test-post-test design, two paper-and-pencil tests and three performance assessments were used to examine the acquisition and transfer of inquiry skills. Additionally, questionnaires were used to measure metacognitive skills. The results of a multilevel analysis controlling for pre-tests, general cognitive ability, age, gender and grade level indicated that explicit instruction facilitates the acquisition of science inquiry skills. Specifically on the performance assessment with an unfamiliar topic, students in the explicit condition outperformed students of both the implicit and baseline condition. Therefore, this study provides a strong argument for including an explicit teaching method for developing inquiry skills in primary science education.