This paper aims to assess and deal with the challenges experienced by medical professionals caring for infectious diseases. In Pakistan, public health is still a serious concern and the main contributor to morbidity and mortality is infectious diseases. The major issue is a resemblance in the clinical symptoms of infectious diseases such as tuberculosis, hepatitis, COVID-19, dengue, and malaria. Early detection of infectious disease is crucial in order to start treatment with counseling and medication. This can only be done if several infections with similar clinical traits can be diagnosed depending on several criteria, including the availability of various kits, the ability to carry out diagnostic procedures, money, and technical staff. But woefully Pakistan's economy is badly battered due to several circumstances. Therefore, we are unable to provide patients with enough diagnostic testing kits and broadly accessible therapy choices, which makes diagnosis more difficult and create hesitancy with fuzziness and randomness. For this purpose, we introduced the new concept of the complex probabilistic hesitant fuzzy N-soft set. We defined its fundamental operations (like restricted and extended union, restricted and extended intersection, weak, top and bottom weak complements, as well as soft max-AND or soft min-OR) with examples. We also discussed their many properties with their proofs and theorems. Furthermore, we developed the algorithms for decision-making where doctors use the complex probabilistic hesitant fuzzy N-soft information to identify a particular disease. Furthermore, we explained numerical illustration of two case studies. Moreover, a sensitive and comparative analysis is discussed. In the last, we conclude the whole study.