Whipple’s disease is a multisystemic disease caused by Tropheryma (T.) whipplei that primarily affects the gastrointestinal tract. In literature, T. whipplei can also cause pulmonary infections. The detection of T. whipplei depends on nucleic acid-based test. With the application of next-generation sequencing (NGS), cases with T. whipplei detected from respiratory tract samples by NGS are increasingly found but there is lack of recognized diagnostic criteria for these cases. Within the context, we propose a grading diagnostic scheme for the situation that T. whipplei is detected from respiratory tract samples, based on clinical experience and diagnostic thinking, and referring to the international classifications of invasive fungal infections. The scheme comprises five levels: confirmed, probable, possible, impossible, and excluded. There were 26 such cases from West China Hospital of Sichuan University and we used our diagnostic scheme to define probable in 6 cases, possible in 9 cases, impossible in 8 cases, and excluded in 3 cases. Based on this, we also propose specific suggestions for sample collection and testing, patient management, and further research directions. These recommendations are preliminary based on the existing cases from West China Hospital of Sichuan University and therefore needs to be verified, modified, optimized, and even reconstructed when more clinical evidence and further clinical studies become available.