Pusat Inovasi Teknologi Sebelas Maret University (PIT UNS) is a university incubator that organizes technology transfer activity in Sebelas Maret University (UNS), Indonesia. The main goal of PIT UNS is to create a technology-based startup from UNS research results. As a new incubator, it is necessary to develop the system of technology-based startup development. This paper aims to conduct the development of the system by benchmarking study. The study starts with the identification of benchmarking target and subject. Then the data is collected, analyzed and integrated with a condition in PIT UNS to determine the best practice. After that, it is developed to create a framework system if technology-based startup development in PIT UNS. The system is validated by Focus Group Discussion and pre-implemented by using case study. The result generates a framework with seven main activities and eight Standard Operation Procedures (SOPs). From that framework, PIT officer and tenant able to identify the incubation position based on their feedback. In addition, management’s element analysis shows that the system should be supported by enhanced quality resources.