Brijendra (20) had left his house in October 2013 on the pretext of attending an army recruitment rally and had been missing since then.
The police recovered his body on Friday after locals complained of foul smell emanating from the well.
A call letter of army recruitment rally, held here in October last year, was also recovered by the police.
On this basis, the relatives of the deceased were contacted, police said.
The body has been sent for post-mortem, police said.