DRAFT prospect Charlie Spargo will have shoulder surgery this week that will rule him out for the rest of the season.

The midfielder suffered the injury in the opening round of the NAB AFL Under-18 Championships while playing for the Allies, and has missed the past two matches.

Spargo, whose father Paul played 81 games for North Melbourne and nine with the Brisbane Bears, will undergo a reconstruction and be sidelined for the remainder of 2017.

The 17-year-old was weighing up whether to play on to further press his draft claims, but NAB AFL Academy coach Luke Power said the decision to go under the knife was taken with a long-term view.

"He had an episode against Vic Country in the first round with the shoulder and it was decided the best course of action is to have it operated on so that, if he does get drafted, he can hit the ground running at an AFL club in the pre-season," Power said.

"He's a really good little player and you can see how much the Allies have missed him in the past two weeks he hasn't played.

"Charlie's played a lot of school footy this year but I don't think it matters too much where he plays, because of his intensity around the ball."

Spargo, who boards at Melbourne Grammar, is originally from Albury, where he was zoned to Greater Western Sydney through its academy region.

However, the Giants lost priority access to him earlier this season when their academy boundaries were realigned by the AFL. He is now a part of the open draft pool.

At 173cm Spargo is one of the shorter midfielders available, however he has impressed over several years with his tenacious and hard-working approach.

In 2015 Spargo claimed the Alan McLean Medal as the best player for the division two under-16 national carnival.