Coach Luis Norton de Matos had suggested four names and had asked each of the 27 players in the team to write on a sheet of paper their choice for captaincy.
The first name would get five points, the next three and the final choice one.
The players unanimously voted for Amarjit as their captain for the FIFA Under-17 World Cup which begins in New Delhi on October 6.
Jitendra Singh, who was second, will be Amarjit's deputy.
While, Suresh Singh, who led India at the AFC Under-16 Championship last year, received the third highest votes.
Defender Sanjeev Stalin finished fourth, an AIFF official said.
Born and brought up in Manipur, Amarjit was introduced to the game by his uncle and he soon found himself at the Chandigarh Football Academy (CFA).
When the selectors were hunting for players to represent India at the Under-17 World Cup, Amarjit was invited for trials and he caught everyone's eye with his good showing.
At first he was slotted with the reserve side and made the first team grade after German coach Nicolai Adam was impressed with his abilities in midfield.
Image: Amarjit Singh in action
Photograph: IndianFootballTeam/Twitter
Watch out for this Brazilian wonderkid at U-17 World Cup!
'U-17 World Cup can have a big impact on Indian football'
How Under-17 World Cup can benefit India's youngsters...
FIFA U-17 World Cup: Pollution in Delhi a big worry
7 women support referees to officiate at Under-17 World Cup