Environmental performance assessment in the civil service has several measuring instruments, among other things, such as DP3, “Functional Position”, and various other measurement tools. As one measure of “Functional Position” that there is “Functional Position for Engineers” to civil engineers engaged in technology and industrial development. Agency for the Assessment and Application of Technology is an agency appointed by the government as a builder of “Functional Position for Engineers” (JFP) since 2007. If there is measurement for officer performance appraisal, then so does the performance assessment of a government agency known by the system of “Government Performance Accountability Report” (LAKIP). However, until now at BPPT, there are no synergies between the two measuring devices to improve the quality both in terms of supporting institutions and human resources. In this thesis we will discuss the implementation approach of Soft System Methodology (SSM) for the design of Enterprise Architecture (EA) in the case study-based employee performance appraisal system that is able to “Functional Position for Engineers” support systems “LAKIP” which is expected to be the solution for increasing input employee performance.