The study investigated the influence of metacognition on critical thinking skills. It is hypothesized in the study that critical thinking occurs when individuals use their underlying metacognitive skills and strategies that increase the probability of a desirable outcome. The Metacognitive Assessment Inventory (MAI) by Schraw and Dennison (Contemporary Educational Psychology 19:460-475, 1994), which measures regulation of cognition and knowledge of cognition, and the Watson-Glaser Critical Thinking Appraisal (WGCTA) with the factors inference, recognition of assumptions, deduction, interpretations, and evaluation of arguments were administered to 240 college students from different universities in the National Capital Region in the Philippines. The Structural Equations Modeling (SEM) was used to determine the effect of metacognition on critical thinking as latent variables. Two models were tested: (1) In the first model, metacognition is composed of two factors while (2) in the second model, metacognition has eight factors as they affect critical thinking. The results indicated that in both models, metacognition has a significant path to critical thinking, p less than 0.05. The analysis also showed that for both metacognition and critical thinking, all underlying factors are significant. The second model had a better goodness of fit as compared with the first as shown by the RMSEA value and other fit indices.