One of the most perplexing dilemmas in modern science is chronic fatigue syndrome (CFS). Even though the illness was recognized at the beginning of the 20th century, the pathogenicity and etiology of the disease remain unknown. We describe an open-inquiry case study on CFS that we have used in our biology classrooms to increase students' critical-thinking skills and understanding of scientific method. Three general categories of potential pathogens – virus, vaccine, and microbiome – are discussed during multiple classroom sessions. We found that our students were more proactive than expected. They researched credible references from the most recent publications and formulated arguments on the medical issue. They applied knowledge of human body systems to explain the complexity of the disease. Students were capable of distinguishing “correlation” and “cause” relations between the disease and pathogens. We observed a high level of student participation and involvement, which not only increased their knowledge of scientific approaches but also strengthened their interaction and communication skills. The case study is suitable for biology courses in both high school and college.