The diagnosis is made primarily on the basis of the patient's symptoms and the knowledge of the kinds of illnesses endemic to a particular geographic region.

Most diagnostic techniques for Japanese encephalitis do not yield results very quickly. Immunofluorescence tests, where special viral markers react with human antibodies that have been tagged with a fluorescent chemical, are used to verify the disease.

However, these results tend to be unavailable until week two of the infection. Other tests involve comparing the presence and quantity of particular antibodies in the blood or spinal fluid during week one with those present during week two of the illness.

Basic clinical tests done:

1. Routine blood examination: To detect any significant changes in the blood cell and its associated components.

2. Examination of cerebro-spinal fluid (CSF):

Detection of cells, indicative of infection.

Elevation of the levels of CSF protein in about 50% of cases

3. Radiological examination:

Computed Tomography

Magnetic Resonance Imaging
To reflect changes in certain regions of the brain and to correlate with the symptoms of the patient.

4. Serological testing:

Immunofluorescence tests, where special viral markers react with human antibodies that have been tagged with a fluorescent chemical, are used to verify the disease.