This study investigated development of students' scientific argumentation levels in the applications made with Problem-Based Computer-Aided Material (PBCAM) designed about Human Endocrine System. The case study method was used: The study group was formed of 43 students in the 11th grade of the science high school in Rize. Human Endocrine System Argumentation Texts (HESAT) was used to determine the students' scientific argumentation levels made before and after the applications with PBCAM. Besides, "PBCAM Student Records" were investigated to determine students' scientific argumentation levels on three different problems in relation to Human Endocrine System during the applications with PBCAM. Within the scope of the research problem, semi-structured interviews were made with 10 students among the participants after the application as well. Students' scientific argumentation levels were assessed with a rubric prepared by one of researchers within the framework of the scientific discussion model Sampson and Clark. The qualitative results indicated that: applications made with PBCAM improved students' skills for presenting claims, proofs, reasoning and conceptual quality of the claims in scientific argumentation. Also, it was seen that "the Observation" section presented as a source of information in the PBCAM was effective on improving students' conceptual understanding. From this point of view, similar applications can be used also in teaching other biology subjects similar to endocrine system topic, which does not provide opportunities to conduct experiments and observations and which is hard to understand.