There are records of lodges conferring the degree of "Scots Master" or "Scotch Master" as early as 1733. A lodge at Temple Bar in London is the earliest such one on record. Other lodges include a lodge at Bath in 1735 and the French lodge, St. George de l'Observance No. 49 at Covent Garden in 1736. The references to these few occasions indicate that these were special meetings held for the purpose of performing unusual ceremonies, probably by visiting Freemasons. The Copiale cipher, dating from the 1730s, says, "The rank of a Scottish Master is an entirely new invention..."

A French trader, by the name of Etienne Morin, had been involved in high degree Masonry in Bordeaux since 1744 and, in 1747, founded an "Ecossais" lodge (Scots Masters Lodge) in the city of Le Cap Français on the north coast of the French colony of Saint-Domingue (now Haiti).  Over the next decade high degree Freemasonry continued to spread to the Western hemisphere as the high degree lodge at Bordeaux warranted or recognized seven Ecossais lodges there. In Paris in 1761, a patent was issued to Etienne Morin, dated 27 August, creating him "Grand Inspector for all parts of the New World". This Patent was signed by officials of the Grand Lodge at Paris and appears to have originally granted him power over the craft lodges only and not over the high or "Ecossais" degree lodges. Later copies of this Patent appear to have been embellished, probably by Morin, to improve his position over the high degree lodges in the West Indies.

Early writers long believed that a "Rite of Perfection" consisting of 25 degrees, the highest being the "Sublime Prince of the Royal Secret" and being the predecessor of the Scottish Rite, had been formed in Paris by a high degree council calling itself "The Council of Emperors of the East and West." The title "Rite of Perfection" first appeared in the Preface to the "Grand Constitutions of 1786," the authority for which is now known to be faulty. It is now generally accepted that this Rite of Twenty-Five degrees was compiled by Etienne Morin and is more properly called "The Rite of the Royal Secret" or "Morin's Rite."  However it was known as "The Order of Prince of the Royal Secret" by the founders of the Scottish Rite who mentioned it in their "Circular throughout the two Hemispheres" or "Manifesto" issued on December 4, 1802.

Morin returned to the West Indies in 1762 or 1763, to Saint-Domingue, where armed with his new Patent he assumed powers to constitute lodges of all degrees, spreading the high degrees throughout the West Indies and North America. Morin stayed in Saint-Domingue until 1766 when he moved to Jamaica. At Kingston, Jamaica in 1770 Morin created a "Grand Chapter" of his new Rite (the Grand Council of Jamaica).  Morin died in 1771 and was buried in Kingston.

The one man who was most important in assisting Morin in spreading the degrees in the New World was a naturalized French subject of Dutch origin named Henry Andrew Francken. Morin appointed him Deputy Grand Inspector General as one of his first acts after returning to the West Indies. Francken worked closely with Morin and, in 1771, produced a manuscript book giving the rituals for the 15th through the 25th degrees. Francken produced at least two more similar manuscripts, one in 1783 and another about 1786. The second and third of these manuscripts included all the degrees from the 4th through the 25th.

A Loge de Parfaits d' Écosse was formed on 12 April 1764 at New Orleans becoming the first high degree lodge on the North American continent. Its life, however, was short as the Treaty of Paris (1763) ceded New Orleans to Spain and the Spanish crown had been historically hostile to Freemasonry. Documented Masonic activity ceased for a time and did not return to New Orleans until the 1790s.

Francken traveled to New York in 1767 where he granted a Patent, dated 26 December 1767, for the formation of a Lodge of Perfection at Albany which was called "Ineffable Lodge of Perfection". This marked the first time the Degrees of Perfection (the 4th through the 14th) were conferred in one of the thirteen British colonies. This Patent, and the early minutes of the Lodge, are still extant and are in the archives of Supreme Council, Northern Jurisdiction.

In 1813 the Supreme Council for the Northern Masonic Jurisdiction was established in New York after a careful inspection of five bodies up to and including the Thirty-Third.  None of these bodies had been sponsored by the Supreme Council at Charleston.

The organization was effected by Emanuel De La Motta, Illustrious Treasurer General, under the direction of John Mitchell, Sovereign Grand Commander, and Frederick Dalcho, Lieutenant Grand Commander of the Supreme Council at Charleston.  The task of sifting through five bodies was a difficult one.  Nevertheless on August 5, 1813, in the city of New York this second Supreme Council in the U.S.A. was established.  On August 5th, 1813 Daniel D. Tompkins was chosen as the first Sovereign Grand Commander of the Northern Masonic Jurisdiction. Tompkins had enjoyed a successful political career. In 1804 he was simultaneously elected to Congress and appointed to the New York Supreme Court. He chose the latter, serving until his election as Governor in 1807. He was offered the post of Secretary of State in the Madison administration and was elected U.S. Vice President in 1816 with fellow Mason James Monroe.

From 1832-1843 the Supreme Council was being held together chiefly through the efforts of John Joseph Gourgas, Grand Secretary from 1813 to 1832 and Sovereign Grand Commander from 1832 until 1851.  Eventually the Scottish Rite once more began to function, but now in the Northern Jurisdiction under divided leadership, Cerneau, Atwood, Hayes, Raymond and others attempted to establish Supreme Scottish Rite Bodies.  In 1860 three were active; each called itself a Supreme Council, and claimed absolute authority.

Fortunately, wise council and Masonic principles prevailed over personal ambitions.  After much preliminary communication, the two Supreme Councils then remaining, the legitimate one headed by Killian H. VanRensselaer, and the recently consolidated Hayes-Raymond Council, met in Boston May 17, 1867, and dissolved their respective Supreme Councils and formed our present supreme Council in the Northern Masonic Jurisdiction.

Henry L. Palmer was elected Sovereign Grand Commander in 1879, beginning the longest tenure (30 years) in the history of the Rite. 
  
In 1921 Leon Abbott was elected Sovereign Grand Commander and moves the Supreme Council offices from New York to Boston. Upon his death, his Will provides for the Abbott Scholarships.
  
Melvin Maynard Johnson was elected Sovereign Grand Commander in 1933 and serves as the first full-time Sovereign Grand Commander. Johnson leads the Rite through the Great Depression, World War II, a membership drop to 208,000, and its rebound to 422,000. He establishes a foundation to fund schizophrenia research and writes many papers on early Freemasonry.
  
In 1968, Sovereign Grand Commander George A. Newbury moves the Supreme Council headquarters from Boston to Lexington, MA, just a mile from where the American Revolution began.
  
The Northern Light began publishing in 1970. 
  
On April 20, 1975, the day after the American Revolution Bicentennial began on Lexington Green, with President Ford presiding, the National Heritage Museum opens on the grounds of Supreme Council headquarters. It is called the gift of the Scottish Rite Masons to the nation.

In 1995, Sovereign Grand Commander Robert O. Ralston began a new charity as the first 32° Masonic Learning Center for Children with Dyslexia opens.
  
The Supreme Council opened its new headquarters building in 2000 on the grounds in Lexington, MA.
  
Walter E. Webber succeeded Robert O. Ralston in 2003 as Sovereign Grand Commander.
  
In 2005 the number of children's learning centers exceeded 50. John Wm. McNaughton succeeded Walter E. Webber in 2006 as Sovereign Grand Commander.