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Background: The Indonesian government has evaluated the research performance of universities, whose measurement process is projected into resources, management, outputs, and revenues to determine the provision of incentives, grants, and program funding to universities. However, efficiency calculations have shown that the outputs and competition-based incentives that drive scientific productivity are more complex. The most competitive systems must also be the most productive when considering resources. Objectives: This study aimed to analyze the research efficiency in the Indonesian higher education system. Research Designs: The efficiency was analyzed by maximizing the 13 product outputs from the research budget and university staff. The result was then compared with the existing performance measurement analysis. Data Envelopment Analysis (DEA) was used to evaluate the efficiency based on the data of 47 universities in the Mandiri cluster and 144 in the Utama cluster for the 2014–2018 period. Results: These findings showed that about 68% of universities have an efficiency value of 1 for the Mandiri group, almost 40% in the Utama group, and 41% for the two groups combined. Additionally, this study compared the efficiency analysis and the impact of the performance evaluation. Conclusions: The comparison showed that adding efficiency or productivity factors in the performance evaluation assessment produced a more accurate result.