Critical thinking (CT) is widely regarded as an important competence to obtain in education. Students’ exposure to problems and collaboration have been proven helpful in promoting CT processes. These elements are present in student-centered instructional environments such as problem-based and project-based learning (P(j)BL). Next to CT, also higher-order thinking (HOT) and critical-analytic thinking (CAT) contain elements that are present in and fostered by P(j)BL. However, HOT, CT, and CAT definitions are often ill-defined and overlap. The present systematic review, therefore, investigated how HOT, CT, and CAT were conceptualized in P(j)BL environments. Another aim of this study was to review the evidence on the effectiveness of P(j)BL environments in fostering HOT, CT, or CAT. Results demonstrated an absence of CAT in P(j)BL research and a stronger focus on CT processes than CT dispositions (i.e., trait-like tendency or willingness to engage in CT). Further, while we found positive effects of P(j)BL on HOT and CT, there was a lack of clarity and consistency in how researchers conceptualized and measured these forms of thinking. Also, essential components of P(j)BL were often overlooked. Finally, we identified various design issues in effect studies, such as the lack of control groups, that bring the reported outcomes of those investigations into question.