Risk management is a key activity in every organization. The identification and evaluation of all risks in higher education institutions lead to the continuous monitoring of investments in people, high technology, and innovation. This paper evaluates the relative efficiency of study programs in Romanian higher education using the DEA method. This study is based on 38 study programs from a public university in Romania, using a traditional DEA approach: CRS-DEA and VRS-DEA models, with an output orientation for three academic years (2016–2019). To avoid distortions in the efficiency scores, we decided to implement the bootstrap method to correct DEA efficiencies. The results show that only four study programs were efficient during this period under the CRS-DEA approach, and eight study programs were efficient under the VRS-DEA model. According to scale efficiency and the bootstrap method, the results also showed that four study programs were efficient during the period analyzed. Finally, we observed that the inefficiency of study programs is relatively persistent (89%), compared with efficient DMUs (11%). Based on these findings, higher education institutions should consider the possibility of increasing the quality of study programs correlated with the degree of attractiveness of various programs in the current socio-economic environment.