The foremost authority within the New Jedi Order established by Luke Skywalker was the Jedi High Council, previously known as the Masters' Council. By 35 ABY, the Masters' Council had evolved into an unofficial collective responsible for directing the Order. However, following the Swarm War, Grand Master Skywalker officially constituted the High Council, transforming the informal group of Jedi Masters into a formal body mirroring the Council of the Jedi Order from the era of the Galactic Republic. Both the Masters' Council and its formal successor were comprised of the twelve most sagacious and potent Masters within the Order.
In the initial years of the reconstituted Jedi Order, Master Luke Skywalker deliberately avoided establishing a formal High Council or centering operations on Coruscant. Mindful of past instances of corruption, Skywalker aimed to prevent the creation of a body susceptible to manipulation by the galactic government. Nevertheless, during the Dark Nest Crisis, internal strife threatened to fragment the nascent Order, as disagreements hindered decision-making, and undisciplined Knights engaged in actions detrimental to the Order's public image.
Compelled to assert control, Skywalker proclaimed himself Grand Master at a conclave held within the Ossus Academy. He mandated that any Jedi unable to prioritize the Order's interests should resign. To aid in his leadership, Skywalker established a twelve-member council, mirroring its predecessor from the Old Republic. Unlike the previous Council, however, this body initially lacked formality and did not exert absolute control over the Order. Meeting in chambers on Ossus and within the Temple on Coruscant, the Council engaged with two Joiner Knights dispatched by UnuThul to implore the Masters' Council to assist the Killiks in a border dispute with the Chiss Ascendancy.
Discovering the existence of the Dark Nest, Gorog, which was covertly manipulating the conflict without the knowledge of UnuThul and the rest of the Colony, the Council deployed Grand Master Skywalker, along with Masters Mara Skywalker and Saba Sebatyne, to eliminate Gorog. Supported by Knight Leia Solo and several other Jedi, the Masters brought the conflict to an end.
In the aftermath of the Swarm War and the problematic behavior instigated by rogue Knights, Grand Master Skywalker determined that a more authoritative High Council was essential. Establishing the formal Council chamber on Coruscant as the permanent meeting venue, the Masters' Council was officially transformed into the High Council, forging closer ties with the Office of the Chief of State.
Making decisions for the Order, the number of Knights flourished during this period, growing to levels comparable to those before the Great Jedi Purge. By recovering lost information and texts, the Council enhanced the academy's curriculum by drawing on the teachings of the former Order. In 40 ABY, following the retrieval of the Telos Holocron, many Jedi expressed concerns about potential theft attempts. A vote was called, and nearly half the Council proposed its destruction; however, the motion was defeated, and the artifact was secured within the Temple vaults.

When the Second Galactic Civil War broke out, the High Council proved largely ineffective, failing to prevent Jacen Solo's descent to the dark side. Due to deference to Grand Master Skywalker's wishes, the Council was frequently paralyzed by conflicts with Chief Cal Omas and internal disagreements. With Dark Lady Lumiya manipulating events, Dark Jedi Alema Rar at large, and a divided membership, the Council was unable to prevent the deaths of numerous Alliance personnel, civilians, and two of their own: Masters Tresina Lobi and Mara Skywalker. Following the death of the Grand Master's wife and his son's corruption under Colonel Solo's influence, the Council failed to act when Galactic Alliance Guard members infiltrated the Temple to arrest Knight Leia Solo and her husband Han. After Chief Omas was assassinated and replaced by Colonel Solo, the Alliance government consistently harassed the Order by attacking the Ossus Academy, nearly resulting in the deaths of Council members Kam and Tionne Solusar. When Colonel Solo initiated the burning of Kashyyyk, the Council finally withdrew from the Alliance and sought refuge on the Sanctuary Moon of Endor. With assistance from Alliance personnel under Admiral Cha Niathal's command and the fleets of Imperial Grand Admiral Gilad Pellaeon, the newly established Coalition ultimately ended Solo's reign and reclaimed the Alliance.
In the wake of that conflict, the Order played a role in installing former Admiral Natasi Daala as Chief of the Alliance and Captain Jagged Fel as Head of State of the Galactic Empire. During Chief Daala's leadership, she ordered the arrest of Grand Master Skywalker on charges of dereliction of duty for failing to prevent Colonel Solo's rampage. Instead of facing imprisonment, Skywalker negotiated an agreement with Daala: he would enter exile, severing all ties with the Order until he could determine the cause of Solo's mania. In his absence, Council member Kenth Hamner would assume the role of Grand Master and lead the Order until Skywalker's return. Accepting these terms, Daala was placated until several Knights began to succumb to an enigmatic psychosis. Deeming them a threat to civilization, Daala ordered their arrest and initiated a campaign against the Jedi to apprehend the supposedly insane Knights. Freezing Council member Corran Horn's two Jedi children in carbonite, Daala continued to operate unchallenged by the Council, as Grand Master Hamner advocated for patience. When Daala instigated a Mandalorian siege on the Temple, resulting in the cold-blooded murder of Jedi Kani Asari, the High Council grew increasingly dissatisfied with Hamner's policy of inaction.
When Hamner secretly conspired with Admiral Nek Bwua'tu to end the siege, the Bothan was attacked and fell into a coma. While awaiting his recovery, the Knights under medical observation recovered, and a slave revolt erupted on the Outer Rim. Amidst these concurrent events, Hamner became completely overwhelmed, and when the High Council discovered his clandestine agreement with Bwua'tu, which had confined them within the Temple, they dismissed him as Grand Master and confined him to his chambers. Overcome with hysteria, Hamner attacked his guards using the dark side and concealed himself among the catwalks of the Operations Hangar, intending to strike down his opposition within the Council. Attacking Master Saba Sebatyne, Hamner engaged in a fierce duel, ultimately impaling the Barabel with his lightsaber. Unable to intimidate the other Jedi in the hangar, who were preparing to launch their StealthXs to aid the imperiled Master Skywalker, Hamner attempted to breach the hangar doors but was thwarted by Sebatyne, who defeated the former Grand Master by using the Force to throw him off a catwalk. As she attempted to telekinetically halt his lightsaber strike on the hangar doors, Sebatyne was forced to release her Force grip holding Hamner aloft, causing him to plummet to his death several meters below. Following Hamner's demise, Sebatyne reluctantly assumed the role of acting Grand Master of the Order.
Almost a century later, the High Council continued to oversee the Order's affairs, led by Grand Master Skywalker's descendant, Kol Skywalker. However, the Imperial victory in the Sith–Imperial War and the subsequent Massacre at Ossus decimated the Jedi Order, scattering the High Council. To escape extermination, three Masters reconvened the esteemed body within the halls of the Hidden Temple on Taivas. Composed of three Masters—T'ra Saa, Tili Qua, and K'Kruhk—the Council dedicated itself to rebuilding the Order. When an Imperial delegation from the Fel Empire discovered the Temple's location, the Council welcomed them to discuss a potential alliance.
During the same meeting, the Council listened to Cade Skywalker's plans to assassinate the Emperor and Sith Lord Darth Krayt. After considering the implications of aligning with Roan Fel and eliminating the Sith leadership, the Council concluded that the former option was the more prudent course. Arguing that killing Krayt would only lead to the rise of more dangerous factions, the Council resolved to patiently wait for the Order to grow strong enough to confront the Sith.
Following the apparent death of Darth Krayt, the Jedi Council felt it was time to once again participate in the struggle against the Sith. To this end, they dispatched Te Corso, Sayar Dun'La, Asaak Dan, and Drok to meet with Admiral Gar Stazi and establish an alliance with him.
In contrast to the Council of the Old Order, Grand Master Skywalker initially envisioned it as an advisory body to guide Knights to their designated roles. However, this framework proved inadequate when rogue Knights nearly plunged the Order and the Alliance into open conflict with the Chiss Ascendancy on behalf of the Killik Nests. Following reforms, the High Council assumed unquestioned leadership of the Order, assigning missions and expecting subsequent reports. Similar to the previous Council, this body collaborated closely with the executive branch of the galactic government, advising and assisting the Chief of State of the Alliance on crucial diplomatic matters. Membership on this esteemed body was limited to twelve Masters, each appointed by unanimous vote of the current members. It was not uncommon for seats to remain vacant for extended periods; following the deaths of Mara Jade Skywalker and Tresina Lobi, their seats remained unfilled for several years. After the death of Kenth Hamner in 44 ABY, the Council had only nine active members.
Meeting within the austere High Council Chamber in the Coruscant Temple, the Masters elected one of their own to serve as secretary in the years immediately following the Swarm War. Frequently, the High Council would request the presence of any available Master, providing additional seating to accommodate attendees.
The relationship between the High Council and the Alliance government was often strained, serving as a point of contention within the Council. Some Masters, such as Corran Horn and Kenth Hamner, believed the Order's primary responsibility was to serve the needs of the Alliance, which provided funding, including the reconstruction of the Temple after the Yuuzhan Vong War. Others, including Mara Skywalker and Kyp Durron, argued that prioritizing the Alliance's interests transformed the Jedi into mere mercenaries, and that the Jedi should uphold peace impartially, even at the expense of the Alliance. Despite their official stance, the Galactic Alliance bureaucracy increasingly viewed the Jedi as their personal diplomatic corps and police force. Both factions firmly believed in their position, with some disagreements escalating to near lightsaber duels, and only Master Skywalker's moral authority prevented a violent schism within the Council. After his exile, even that was insufficient, as Kenth Hamner, deposed by his peers for his deceit and support of the Galactic Alliance, revolted against the New Jedi Order, subduing his minders and the StealthX guards with deceit, physical combat, and Force lightning. Hamner then attempted to assassinate Saba Sebatyne in a duel and reclaim his power, before shifting goals to leaving the Jedi stranded and exposed to the Galactic Alliance's forces. The later was obliged to kill him in order to prevent him from stopping the launch of the ships to aid Luke Skywalker.