Viral encephalitis/meningitis is a severe inflammatory disease of the central nervous system that poses a significant threat to public health. Despite the crucial role played by medical history, symptoms, routine tests and imaging in its diagnosis, and continuous improvements in molecular diagnostic techniques, limitations including technical limitations, assay variability, sample types, and detection time windows still constrain its diagnosis. Moreover, the selection of appropriate diagnostic techniques depends on different clinical features, leaving 40% to 60% of patients with an unclear etiology. Timely and accurate diagnosis is fundamental for initiating targeted and appropriate treatment. Sixty to eighty percent of patients with viral encephalitis initially seek medical attention at primary healthcare institutions. However, due to technical constraints, the diagnostic rate in these institutions is below 20%. Therefore, establishing a standardized diagnostic pathway based on etiology and implementing a tiered diagnostic strategy are particularly necessary. In situations where resources are limited at primary healthcare institutions, the preliminary diagnosis can be established by detailed inquiry into medical history, comprehensive physical examination, and basic laboratory tests. Based on the suspected etiology, routine molecular biology techniques such as polymerase chain reaction (PCR) can be employed for initial pathogen screening. In cases whose PCR results are negative or not feasible, non-targeted broad-coverage techniques like metagenomic next-generation sequencing (mNGS) should be considered. The establishment of a multidisciplinary team for diagnosis and treatment, along with the creation of clinical diagnostic and treatment networks, are essential to enhance the diagnostic rate and improve clinical outcomes. With advancements in diagnostic technologies and the application of artificial intelligence, the diagnosis of viral encephalitis is expected to become more precise.