As a result of the Northeast Region Realignment of 1988, Monaken Lodge #103 from NE-5B and Ho-Nan-Ne-Ho-Ont Lodge #165 from NE-2C were added, making a total of ten lodges in the newly formed Section NE-5. Gyantwachia Lodge #255 hosted the first Section Five conclave in 1989 at Custaloga Town Scout Reservation.

In 1993, Kiasutha Lodge #57 and Tanacharison Lodge #67 merged to form Enda Lechauhanne Lodge #57. As a result of the 1994 region realignment, Ahtuhquog Lodge #540 re-joined its brothers from Area 3-F, and Section Five was back to 10 lodges.