Conducting scientific inquiry is expected to help students make informed decisions; however, how exactly it can help is rarely explained in science education standards. According to classroom studies, inquiry that students conduct in science classes seems to have little effect on their decision-making. Predetermined values play a large role in students' decision-making, but students do not explore these values or evaluate whether they are appropriate to the particular issue they are deciding, and they often ignore relevant scientific information. We explore how to connect inquiry and values, and how this connection can contribute to informed decision-making based on John Dewey's philosophy. Dewey argues that scientific inquiry should include value judgments and that conducting inquiry can improve the ability to make good value judgments. Value judgment is essential to informed, rational decision-making, and Dewey's ideas can explain how conducting inquiry can contribute to make an informed decision through value judgment. According to Dewey, each value judgment during inquiry is a practical judgment guiding action, and students can improve their value judgments by evaluating their actions during scientific inquiry. Thus, we suggest that students need an opportunity to explore values through scientific inquiry and that practicing value judgment will help informed decision-makings.