Originally called St Paul's, this chapel was the first Protestant church in Upper Canada and is now the oldest surviving church in Ontario. It is the only Royal Chapel in North America.

Built by the Crown in 1785, it was given to those Mohawk Indians led by Joseph Brant who had supported the British during the American Revolution. Their choice cost them their lands in New York. To compensate for the loss the Mohawks were granted 760 000 acres on the Grand River complete with two mills, a school and a chapel. Although the church has undergone many alterations, it stands as a reminder of the important role played by the Loyalist Mohawks in the early settlement of Ontario.

The first Chapel of the Mohawks was built at Fort Hunter in 1712 during the reign of Queen Anne. Representatives had made an historic visit to her Court from the Six Nations people, then living in the Mohawk Valley. They pledged their loyalty and Friendship to the Crown, and made a request for a Chapel and Priest.

Consequently, the Queen Anne Chapel was built, and a Minister was provided through the New England Company. Upon completion of construction, Queen Anne presented her Chapel of the Mohawks with a Bible, Silver Communion Service and prayer books. This Chapel was destroyed as an aftermath of the American Revolution.

During this war, many of the Six Nations people, under the leadership of Captain Joseph Brant, chose to ally themselves with those in the Thirteen Colonies who remained Loyal to the British Crown. Upon the defeat of the British Crown Forces, and the formation of the United States of America, the loyal Six Nation people, rather than swerve from their loyalty to the Crown, chose to abandon their homelands in their beloved Mohawk Valley, and moved North into Canada, a British Crown colony.

Through the terms of the Haldimand Treaty of 1784, Joseph Brant secured a land grant for the native loyalists six miles on either side of the Grand River from its source to its mouth. Brant also negotiated for and received a Church, the present St Paul’s, Her Majesty’s Chapel of the Mohawks, built upon the banks of the Grand River in 1785, in the reign of George III. The Mohawk Chapel, as it is commonly known, stands as a shrine to the Six Nations as a symbolic link between the Crown of England and the people of the Grand River Valley.

Mohawks, led by Joseph Brant, established a village of some 400 inhabitants by 1788. The community was situated at an important crossing point on the river ("Brant's Ford") and prospered as a resting place for travellers on the "Detroit Path", a trail linking the Niagara and Detroit rivers. Increasingly, European settlers encroached on Six Nations' lands. In 1841 the government moved the Grand River Iroquois to a section of their land south of the river. Of the Mohawk Village, only the chapel remains.

During the Revolution, the Queen Anne Bible and Silver were buried for safekeeping on the farm of Boyd Hunter. These treasures were recovered and returned to the Mohawk Chapel upon its completion in 1785. The church was dedicated to Saint Paul in 1788 by the Reverend John Stuart. At this time the Communion Silver was divided between the Grand River Mohawks and the Bay of Quinte Mohawks. The Mohawk Chapel Communion Silver and Bible are now in safekeeping. Until 1970 and the closing of the Mohawk Institute, they were kept in the school safe in custody of the Chaplain, and the Communion Silver was used during the regular Communion Services at the Chapel.

The Mohawk Chapel did not have a resident Minister until the arrival of the Rev. Robert Lugger in 1827. He was sent out by the New England Company, who continued their support and interest in the Six Nations people in their new homeland. In 1830, the second Anglican Bishop of Quebec, The Right Reverend Charles Stewart, consecrated the Chapel. Until 1833 The Mohawk Chapel was the only Protestant Church on the Grand River.

In 1841 the Mohawk Village was "surrendered" to the Crown, and the people migrated to the Six Nations Reserve. As a result, the congregation slowly disappeared and shifted their attendance to the Kenyangah Church, St John’s Anglican, on the Reserve.

By this time the Mohawk Institute 1831-1970, a school for first nation boys and girls, had been built by the New England Company, and The Chapel came into use over the years mainly as a school Chapel. The Principal of the school and the Chaplain of the Chapel were usually the same person.

The Chapel slowly fell into a state of disrepair until in 1869 a major renovation was necessary. In 1904 it was given Royal designation by Edward VII. Further extensive (restorations were made in 1939, in the 1960's (as well a., the following years in 1975-1976). In 1983 renovations to the Chapel were completed in anticipation of the Six Nations Bicentennial and the visit of Queen Elizabeth and Prince Philip the following year. At this time a fund for the perpetual care of the Chapel was established.  In 2009 a major stabilization of the roof and floor structures took place, and in 2012 the chapel was made a full accessible site.

In 1850 the remains of Captain Joseph Brant were moved from the original burial site in Burlington, to a tomb at the Mohawk Chapel, re-affirming the Chapels connection with the native people. The remains of Brant's son, John Brant, also rest in the tomb.

Next to Brant's tomb is a boulder, bearing memorial to the Indian poetess, E. Pauline Johnson, who was born at Chiefswood on the Six Nations Reserve, and who attended services in the Chapel.

At the rear of the Chapel there is an observation deck that allows a view of the ox-bow in the Grand River, when the native people disembarked from their canoes when they came to the Chapel Services.

Eight stained glass windows were installed in the Chapel (1959–1962). Each window depicts an event in the history of the Six Nation people. It is possible to imagine the history surrounding this historic spot as one learns, from the story the windows portray.

St Paul's, Her Majesty's Royal Chapel of the Mohawks, is within the Anglican Diocese of Huron. The Chaplain is appointed by the Bishop of Huron.

The Chapel provides a peaceful atmosphere and a unique history that is shared with many welcome visitors from around the world.