D.A. Points (69), Henrik Bjornstadt (69), John B. Holmes (69), Alex Aragon (68) and Greg Kraft (72) are knotted in second place at 6-under-par 138.
Allen, who came in third at Q-school in 2003, played the Crooked Cat course on Thursday and started on the back nine. He birdied the par-5 14th, but that was the last until the second nine.
Allen, who finished 130th on the 2005 PGA Tour money list, bogeyed the 16th, but atoned for the miscue with a eagle at the par-5 17th. The 46-year-old did not build any momentum from the eagle as he bogeyed the 18th to make the turn at 1-under 35.
It was Allen's play at the start of his second nine that padded his large cushion. He birdied three of his first four holes to reach 12 under par. Allen parred out from the fourth and is in strong position to make the PGA Tour for the eighth time in his last 12 appearances in Q-school.
Points, who was a PGA Tour rookie in 2005, mixed four birdies and a bogey at the Panther Lake course. Points is in the final stage for the fifth time in six years, but has yet to earn his card via this route. He finished second on the 2004 Nationwide Tour money list.
Bjornstadt, who can become the first Norwegian to play on the PGA Tour, collected five birdies and two bogeys at Panther Lake. He formerly played the European Tour, but not last year. Through part of the 2005 season, Bjornstadt worked as a carpenter.
Holmes, who graduated this year from the University of Kentucky, had the most up-and-down round of any of the players near the top of the leaderboard. He posted two eagles, four birdies, three bogeys and a double-bogey at the Panther course.
Aragon tallied six birdies and two bogeys at Panther Lake, while Kraft made a sweep among those in second. He also played Panther Lake and was even with three birdies and three bogeys.
Alex Cejka (66), Jeff Overton (71), Peter Tomasulo (69), Danny Ellis (70), Scott Hend (70), Robert Garrigus (71) and Ryan Howison (70) share seventh place at 5-under-par 139.
Ryan Hietala was part of a tie for second place after Wednesday's opening round, but struggled badly on Thursday. He shot a 6-over-par 78 and is now tied for 73rd place at even-par 144.