The present study examined to what extent inquiry-based investigation as an instructional approach associated with students’ overall science achievement and achievement in cognitive domains, including knowing science facts, applying scientific principles, and reasoning with scientific concepts to solve problems. Using TIMSS 2007 science achievement data for the 8th graders in the USA and the corresponding student questionnaires, we found that students’ involvement in inquiry-based scientific investigation negatively related to students’ overall science achievement. As the skills involved higher cognitive abilities, from knowing to applying and reasoning, the more students were engaged in the investigation, the more their achievement scores dropped. In contrast, students’ achievement significantly related to explicit instruction and as the skills involved higher cognitive abilities, the positive significant relationship got more strengthened.