Fleetwood, who leads the second-tier Challenge Tour rankings, shot a 9-under 63 at Kingsbarns, the same course where first-round leader Hoey shot a second straight 66. They both have 12-under totals of 132.
Former British Open champion Louis Oosthuizen is one shot back after a 67 in unseasonably warm conditions at Carnoustie, while 2010 U.S. Open winner Graeme McDowell is tied at 10 under with four others after shooting 67.
Hoey made seven birdies, but Fleetwood rolled in nine in an error-free round after turning in 31 at Kingsbarns, which is producing the lowest scores of the three courses.
"I've watched this tournament on TV for years and I pretty much analyze everything (the top players) do. Obviously, my name is in pretty good company right now," said the 20-year-old Fleetwood, who won a Challenge Tour event in Kazakhstan three weeks ago.
Hoey has already won a title this year -- in Madeira in May -- but capturing the Dunhill Links and a first prize of $800,000 would rank much higher among his achievements.
"It's nice to do well in the big ones, because I did reasonable at Wentworth (31st), too. Hopefully, I can keep going the next two days," the former British amateur champion said.
With little wind in Scotland for the second straight day, most of the high-profile players who went around the usually severe Carnoustie took full advantage.
The sixth-ranked Kaymer, looking to become the first player to successfully defend the title, put himself in contention to break the course record of 64 after eight birdies in 14 holes.
However, bogeys at Nos. 16 and 17 set him back.
"I played very good golf -- it was just not a very good finish. But I'll settle for a 67 at Carnoustie," Kaymer said.
Daniel Gaunt of Australia (65 at Kingsbarns), Markus Brier of Austria (68 at Kingsbarns), Marc Warren of Scotland (68 at St. Andrews) and Jaco van Zyl of South Africa (67 at Carnoustie) were at 10 under with McDowell.
The shot of the day was made by James Byrne, who aced the par-3 No. 13 with a 7 iron from 174 yards.
It put the 22-year-old Scot, who turned professional this month, at 10 under -- momentarily a shot off the lead -- before a closing 7 put him at 6 under.