At the 1992 BSA annual meeting, it was announced that the then Six Region structure would be consolidated into Four Regions. Two years later, the Northeast Region's areas and sections were redrawn to conform to the new regional organization. The existing twelve sections were reshuffled from seven to five areas. Final conclaves for the old sections where held in 1994.

After the 1994 Conclaves, the lodges of NE-3A were divided into two new sections. Ktemaque 15, Tankiteke 313, Achewon Netopalis 427, and Paugassett 553 were transferred to the new Section NE-2A. Ranachqua 4, Shu-Shu-Gah 24, Suanhacky 49, Man-A-Hattin 82, Aquehongian 112, Shinnecock 360, Buckskin 412, Yokahú 506 and Arawak 562 become the new Section NE-2C.

As a result of the 1997 realignment, Section NE-3A was reestablished after the 1997 Conclaves. The old Section NE-2A, which had seventeen lodges, lost seven lodges to NE-2A, NE-2B, and NE-3B, and was renamed NE-3A.

Before the 1998 Conclave, Buckskin 412 was moved from NE-2B to NE-3A.

Before the 1998 Conclave, Shinnecock 360 was moved from NE-2B to NE-3A.

October 4, 1998, Tankiteke 313 and Arcoon 369 merged to become Owaneco Lodge #313

On September 1st, 1999, the Northeast Region consolidated from five areas to four (ten sections, down from eleven). The new section boundaries were effective at the conclusion of each section's 2000 conclave. Tschitani 10 was moved from NE-3A to NE-1B. Shinnecock 360 and Buckskin 412 from were moved to Section NE-2B. While the remainder of the old Section NE-3A (Ranachqua 4, Shu-Shu-Gah 24, Suanhacky 49, Man-A-Hattin 82, Aquehongian 112, Owaneco 313, Achewon Netopalis 427, and Paugassett 553) was renamed Section NE-2C. Section NE-5A (TKäen DōD 30, Langundowi 46, Ty-Ohni 95, Ho-De-No-Sau-Nee 159, Ho-Nan-Ne-Ho-Ont 165, Gyantwachia 255, and Ashokwahta 339) is renamed Section NE-3A, and gained Ganeodiyo 417 from NE-5B.

In March 2008, a new realignment for the Northeast Region was announced. New sections went into effect following the 2008 conclaves. As a result of the 2008 Northeast Region Realignment, Section NE-3A gains five eastern New York lodges from NE-3B (Ga-Hon-Ga 34, Otahnagon 172, Kayanernh-Kowa 219, Tahgajute 247, and Onteroraus 402) while the three Pennsylvania lodges (Langundowi 46, Ho-Nan-Ne-Ho-Ont 165, and Gyantwachia 255) are reunited with their brothers from the northern half of the old Section NE-5 to form the new Section NE-4A.

In late 2009, Tahgajute 247 was absorbed by Kayanernh-Kowa 219 after the National Office did not renew Cayuga County Council's (Tahgajute 247) Charter. Lowanne Nimat 219 was formed January 1, 2010 after completion of the absorbtion/merger.

January 31, 2010 - Ty-Ohni 95 and Ganeodiyo 417 merged to form Tschipey Achtu 95.

In May of 2011, a New Section Organization for the Northeast Region was announced. New sections will go into effect following the 2011 conclaves. Section NE-3A loses three lodges (Ga-Hon-Ga 34, Otahnagon 172, and Onteroraus 402) to new Section NE-3B.

In October 2021, National announced that, as part of Project Magellan, the OA would be moving to two regions. Section NE-3A was renamed Section E15.