The Conventional instructional design methods using teacher-centered learning approaches provide few opportunities for students to be actively involved during the learning process. This process is not relevant to the characteristics of the Software Modeling course which ideally emphasizes student-centered learning. As a result, instructors cannot control the learning system efficiently, so students cannot reach the minimum competency standards planned in the learning design. In this work, we propose an instructional design model that integrates Problem-Based Learning (PBL) into the instructional deign of Software Modeling course. Three main elements of the PBL learning system model are proposed, namely: Elementary Curriculum that emphasizes the use of problems as the starting point of student learning; Element Group that emphasizes collaboration systems (group discussion-based learning); and Student Elements that emphasizes the Student-Directed Learning (SDL) system. The three main elements of PBL are applied thoroughly and proportionally to each particular learning topic in Software Modeling course. This concept is different from PBL concepts which have been widely applied as learning models, which do not apply the three main PBL elements to each learning topic. This concept is also designed to improve the weaknesses of the PBL model which only places individual learning in small portions, or even none at all. This research uses the Research and Development (R&D) method which consists of three main stages, namely: analysis of system requirements, system development, and formative evaluation. In formative evaluation we do the expert validation, one-to-one student evaluations, and small group evaluation to test the effectiveness of the system. The result of expert validation (related to content, instructional design, and media design) shows that the instructional media product based on PBL that is developed is very suitable to be used as a learning resource, with an average validation percentage of 83.2%. The students' responses to the one-to-one student evaluation and small group trials show that the instructional design products that are developed are feasible to make student actively involved during the learning process, with an average value (related to product display, Usability, and benefits aspects) reach 82.6%. The average level of mastery of students on certain topics reaches more than 96%.