Twenty-first century and higher-learning skills such as critical thinking are highly desired for new college graduates entering the workplace, especially with rapid changing technology and a more globalized economy. As a result, the importance of critical thinking development at higher education institutions has increased. The purpose of this study was to examine the effect of student and institutional variables on the difference in critical thinking scores between first-year and third/fourth-year students at higher education institutions. We examined the extent to which institutional variables moderate the relationship between student variables and the critical thinking score difference. We used a multi-level modeling approach to account for the clustering of students in institutions. Results of this study showed that: (a) institutional variability accounted for 15% of the variance in estimated critical thinking scores, (b) third/fourth-year students had higher critical thinking scores as compared to their first-year peers even when controlling for college admissions score, and (c) in the final model, the main effects of college admission scores, student-faculty ratio, and percent Black/African American were statistically significant; however, retention was the only significant moderator of the relationship between critical thinking scores and class level. Implications and future research are discussed.