The lopsided Group E match took place at the Indira Gandhi International Stadium.
Nakamura found the back of the net in the 22nd, 30th and 43rd minute.
Takefusa Kubo, dubbed the Japanese Messi for his exceptional skills, added a fourth in the 45th minute. Taisei Miyashiro scored the fifth goal (51st) at the start of the second half and Toichi Suzuki scored the sixth (90th) towards the end of the game.
Patrick Palacios reduced the margin for Honduras by scoring in the 90th minute following a corner.
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Nakamura opened the scoring when he headed in a Kubo cross from a very close range.
The Nakamura-Kubo combination again clicked again eight minutes later as Nakamura's left-footed shot from the centre of the box found the back of the net.
The hat-trick goal was achieved when Nakamura's left- footed attempt off a Soichiro Kozuki through ball hit the target.
It was then the turn of Kubo to enter his name in the score sheet and Nakamura to provide the assist. The script remained pretty much the same in the second half as Japan emerged comfortable winners.
In the 2011 edition, they created a flutter by topping a group that included world football heavyweights Argentina, France and Jamaica on their way to the quarterfinals.
The Asian nation secured a ticket to India by virtue of an impressive performance in the 2016 AFC Under-16 championship.
Honduras have managed to regularly qualify for the tournament since 2007. They were knocked out of the first two editions but managed to reach the quarterfinals in 2013 in the UAE.