The Tribe broke the scoring ice when McCown raced around the right side for a 54-yard touchdown that came with 11:27 to go in the first period.
The Tribe at that time held what turned out to be their only lead of the contest, 7-0, following Ryan Travis' PAT.
With just under six minutes to go in the first half McCown dialed up Claude Franklin for an electrifying 85-yard catch-and-run that pulled the Indians to within six, 20-14.
The Tribe's final points came on a defensive touchdown.
Forest Burton fell on top of a Lion fumble in the end zone with 5:29 to go in the game, which were the visitor's final points of the evening.
Jacksonville was threatening to score deep in Henderson territory late in the second quarter, but a botched trick play on fourth down run out of the wildcat formation with McCown lining up as a slot receiver resulted in an Indian fumble that was recovered by the Lions.
Timothy Boseman, a senior, came up with a fumble recovery for the Tribe
Henderson finished with 420 total yards to 361 by the Tribe.
Jacksonville closes out non-district play next Friday by visiting Marshall (1-3). Kick off is scheduled for 7:30 p.m.at Maverick Stadium.
Henderson 40, Jacksonville 20
Jacksonville 7 7 0 6 — 20
Henderson 20 0 13 7 — 40
J-Carter McCown 54 run (Ryan Travis kick), 11:27
H-Tristan Lary 29 pass from Zane Boles (Edward Sanchez kick), 6:18
H-Seth Hensley recovered blocked punt in end zone (kick failed), 5:49
J-Claude Franklin 85 pass from McCown (Travis kick), 5:54
H-Tre Hollins 18 pass from Boles (pass failed), 7:42
H-Boles 22 run (Sanchez kick), 5:03
H-Tim Hogan 18 run (Sanchez kick), 9:05
J-Forest Burton recovered fumble in end zone (kick failed), 5:29