Kelly won the run last year when competing for a place in the Greater Western Sydney mini-draft, and backed up just over a month before this year’s draft, completeing the run in nine minutes and 32 seconds.
The best time in combine testing is nine minutes and 30 seconds, by former Port Adelaide rookie Tom Rieschbieth in 2005.
The 18-year-old Kelly surpassed his time of last year by 16 seconds, and again underlined himself as an early pick on November 21 when the draft takes place at the Gold Coast.
"I had the advantage of a few weeks of training under my belt and I was hoping to get a bit of a PB (personal best)," Kelly said after the run.
"I'm pretty happy with it. It's a good way to end the camp, it's been a lot of fun this week."
West Australian Nick Robertson ran nine minutes and 46 seconds, which was followed by Collingwood father-son prospect Jake Kelly, who ran nine minutes and 51 seconds.
Robertson and Jake Kelly were also inside the top 10 results of combine testing.
The AFL's national talent manager Kevin Sheehan said Josh Kelly's effort had ended a strong week at Etihad Stadium.
"The game's in great hands when young men, like the 111 we've seen here in the past four days, present themselves in such fantastic condition and all bright-eyed and looking forward to getting a chance in the AFL," Sheehan said.
"I think [Josh Kelly] is an extraordinary young talent as a player, and now you see him as an elite athlete. He ticks every box and on top of that he's just such a coachable young man."
On Monday at 10am, clubs will take part in the father-son bidding process after North Melbourne nominated Luke McDonald as a father-son draftee.
The son of former Kangaroos big man Donald, McDonald is likely to cost the club its first-round selection (pick eight).
The skillful half-back is widely seen as one of the best five or six players in this year's draft pool.
As reported by AFL.com.au this week, Collingwood has nominated Jake Kelly as a provisional father-son pre-selection pick for the rookie draft.
It means that if the son of former Magpies defender Craig does not get picked in the NAB AFL Draft, the Magpies can choose to automatically list him ahead of the rookie draft.
The same will happen for Ryan Lester-Smith, son of Neil, at Fremantle, having been nominated as a rookie father-son pick by the Dockers.
The Brisbane Lions nominated academy player Jonathan Freeman, under rules giving them first access on players developed out of their home state.
But he falls under the same bidding process as McDonald, and if another club bids for him the Lions have the option of matching the bid.
Three-kilometre time trial Minutes Seconds
Kelly, Josh 9 32
Robertson, Nick 9 46
Kelly, Jake 9 51
Tsitas, James 9 54
Byrne-Jones, Darcy 10 00
Drummond, Nathan 10 01
Templeton, Eli 10 05
Pearce, Alex 10 06
Kolodjashnij, Kade 10 10
Freeman, Nathan 10 15