The vaccination drive has been included in the routine vaccination programme for children up to two years, said M P Singh, Chief Medical Officer Gorakhpur.
The free drive began on April 15.
"The families living near the piggeries are given priority as the vector-borne disease spreads through mosquitoes that carry JE viruses," he said.
Pig is the primary host to JE virus.
The disease takes toll of an average 500 lives every year in terai region of Uttar Pradesh.
The National Institute of Virulogy (NIV), Pune has opened a field lab in BRD Medical College here to identify the JE and other viruses causing brain fever in the region.