This article provides an analysis of the academic performance of higher education institutions (HEIs) in Vietnam with 50 universities and 50 colleges in 2011/12. The two-stage semiparametric data envelopment analysis is used to estimate the efficiency of HEIs and investigate the effects of various factors on their performance. The findings reveal that HEIs in the surveyed sample show that there are still potential avenues to improve their existing performance. There appears to be a difference in the efficiencies of public and private HEIs in the reported year. It is noted that the inefficiency of HEIs are not entirely a result of managerial performance, but also influenced by other factors such as location, age and the contribution of tuition fees. Our results are expected to provide more understanding of the operational efficiency of HEIs for educational managers and policymakers to find possible solutions to improve the performance of Vietnamese higher education.