Virtual tools are rapidly supplementing physical tools in classrooms. Although extensive research has compared the benefits of using virtual and physical manipulatives, few studies have systematically explored the learning benefits of using a physical and a virtual tool. As the major learning goal in science, technology, engineering, and mathematics (STEM) education is to help students better understand scientific and mathematical concepts and processes, this study reviewed empirical studies comparing learning performance between working with physical and virtual manipulatives published between 2000 and 2022 in Education and Psychology journals. The results revealed inconsistent patterns in learning comparison across studies even with similar interventions. The discrepancy was reinterpreted based on the amount of information provided by tools, and cognitive engagement calibrated by verbs from instructional directives in the implementation. It was found that learners showed better learning performance when a tool provided more concept-related information and when they engaged in their learning activities more deeply, not whether a physical or a virtual manipulative was used. The implementation guideline for teachers to consider was discussed when they create lesson plans with physical and virtual manipulatives.