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| Timber Trestle Division | |
 Frank Meyer, Herington, Superintendent |
The western terminus of the Flint Hills Nature Trail, this division extends eastward from Herington in Dickinson County to Wilsey, Morris County. It has one mile of trail in use within Herington. |
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Neosho Crossing Division | |
 Scott Allen, Council Grove, Superintendent |
Extending from Wilsey eastward to the Morris County line, the three and a half miles open and in use between Council Grove and Ale-Ga-Wa Park were the first officially opened. A portion of the trail west of Council Grove occupies the original Santa Fe Trail. |
| LyCo Division | |
 Gina Poertner, Emporia, Superintendent |
This division extends from the eastern Morris County line eastward through Lyon County to U.S. 75 Highway in Osage County. There are five miles open and in use between Allen and Bushong. Osage City government secured a TEA-21 grant to develop and pave the trail within its city limits. |
| Landon Nature Trail Division | |
 John Purvis, Topeka, Superintendent |
This division extends south from Topeka in Shawnee County to Lomax Junction in Osage County, where it joins the Flint Hills Nature Trail. There are four plus miles open from the city limits of Topeka to beyond Berryton. Topeka Parks and Recreation Department has undertaken the development of the four and a half miles of trail within the city limits. |
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| Marais de Cygne Division | |
 Dan Pickert, Ottawa, Superintendent |
The division extends eastward from U. S. 75 Highway in Osage County to Rantoul, Franklin County. There are six miles open and in use eastward from U. S. 75 through the village of Vassar; and trail within the city of Ottawa is open, where the Flint Hills Nature Trail intersects with the Prairie Spirit Trail, developed and maintained by Kansas Department of Wildlife and Parks. |
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| Osawatomie Division | |
 Doug Walker, Osawatomie, Superintendent |
The eastern terminus of the Flint HIlls Nature Trail extends from Rantoul, Franklin County to the western edge of Osawatomie, Miami County. Approximately four miles open in Miami and eastern Franklin Counties are open and in use. |
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