The chiefs of the Clan Farquharson trace their ancestry back to Farquhar, fourth son of Alexander "Ciar" Shaw of Rothiemurchus. Alexander Shaw was the fifth chief of the Clan Shaw. His descendants took the name Farquharson. Another of Alexander's sons was Donald, who married Isobel Stewart, the heiress of Invercauld Donald's son was Finla Mor who was the real progenitor of the clan. MacFionlaigh Mor is the Scottish Gaelic patronymic. Finla Mor was the royal banner bearer at the Battle of Pinkie Cleugh in 1547 where he was killed. However he produced nine sons over two marriages from which the important cadet branches of the clan were sprung and the clan grew in stature. In 1595 the Clan Farquhasron joined the Chattan Confederation and a bond of manrent acknowledged the chief of Clan Mackintosh, who was also chief of Clan Chattan as their "natyff cheiff".
Towards the end of the 16th century the Clan Erskine chiefs set out to claim the Earldom of Mar but they were opposed by the increasing power of the Farquharsons. Braemar Castle was built by John Erskine, 18th Earl of Mar but it fell into the hands of the Clan Farquharson. The clan became known as the fighting Farquharsons due to their fierce reputation and they became strong supporters of the Stuarts.
17th century, clan conflicts and Civil War 
During the Scottish Civil War Donald Farquharson of Monaltrie fought for James Graham, 1st Marquess of Montrose in 1644. John Farquharson of Inverey was known as the Black Colonel and burned Braemar Castle. John supported James VII of Scotland and followed John Graham, 1st Viscount Dundee in 1689. After Dundee's death in 1689 the Clan Farquharson supported his successor, Thomas Buchan of the Clan Buchan.
In the late 17th century the Earl of Airlie came into dispute with the Clan MacThomas over the lands of Canlochcan. Airlie's legal action was successful but the chief of Clan MacThomas refused to recognize this and continued to pasture his cattle on the disputed land. In response Airlie used his legal right to lease the land to men of the Clan Farquharson which led to a feud. On the 28 January 1673 Farquharson of Broughdearg was killed along with two sons of the chief of Clan MacThomas. The lawsuits that followed crippled the MacThomas chief.
18th century and Jacobite uprisings 
During the Jacobite rising of 1715 another John Farquharson of Invercauld was a colonel in Chattan Confederation regiment which supported James Francis Edward Stuart. John was taken prisoner at the Battle of Preston (1715). He was held at Marshalsea Prison and was condemned to be executed at the Tower of London, however he and two other highland officers were reprieved on the morning of execution. He was paroled and not allowed to return to Scotland for over twenty years.
In 1745 the strength of the Clan Farquharson was estimated as 500 by Duncan Forbes, Lord Culloden. During the 1745 Jacobite rising, the cousin of John Farquharson was Lady Anne Farquharson-MacKintosh who was wife of Angus Mackintosh, chief of Clan Mackintosh. Angus Mackintosh was in fact a serving officer in the Black Watch regiment of the British Army and he was captured at the Battle of Prestonpans by Jacobite forces. Mackintosh was sent home to Moy having been given parole not to take arms against the Jacobites and when he arrived he was greeted by his wife, Anne Farquharson, who said "Your servant, captain" to which he replied "Your servant, colonel". She was ever after known as Colonel Anne. Anne later saved Charles Edward Stuart from capture in what is known as the Rout of Moy. Anne was imprisoned for six weeks after the Battle of Culloden.
Modern clan 
The Chief of Clan Farquharson is Alwyne Arthur Compton Farquharson of Invercauld, Chief of the Name and Arms of Farquharson, 16th Baron of Invercauld and Omnalprie, MC, JP; as recognised by Lord Lyon King of Arms. Captain Alwyne Arthur Compton Farquharson of Invercauld was by Lyon Court in 1949 confirmed MacFionnlaidh. He served with distinction as a Captain in the Royal Scots Greys during World War Two. Captain Farquharson resides at Valley Farm, Norfolk with his second wife, Madame Patricia Farquharson.
- Inverey Castle was the seat of the chief of Clan Farquharson.
- Kindrochit Castle is a 15thC ruin located within Braemar Village across from the local butchery shop.
- Braemar Castle was attacked and burned by John Farquharson, the Black Colonel of Inverey in 1689, killing John Erskine. The castle was left in ruins until 1748 when it was leased to the government by the Clan Farquharson. The castle is currently undergoing extensive renovations to preserve the structural fabric of the building, which are funded in part by Historic Scotland, Lottery et al grants and supplemented through locally lead fund raising. Many possessions and furnishings of significant historic interest to the Clan Farquharson, Braemar Castle and Scotland as a nation were privately gifted by HRH The Prince Charles, Duke of Rothesay following an auction of Braemar Castle's contents six years ago.
- Invercauld House, traditional seat of the current chief of Clan Farquharson, Captain Alwyne Arthur Compton Farquharson, is currently let to a private tenant.
Clan Profile 
- Crest: On a chapeau Gules furred Ermine, a demi-lion Gules holding in his dexter paw a sword Proper.
- Motto: Fide et Fortitudine ("Fidelity and Fortitude") and (On compartment) I force nae freen, I fear nae foe.
There are several tartans attributed to the name Farquharson.
See also 
- James Logan's The Clans of the Scottish Highlands, 1845
- Way, George and Squire, Romily. Collins Scottish Clan & Family Encyclopedia. (Foreword by The Rt Hon. The Earl of Elgin KT, Convenor, The Standing Council of Scottish Chiefs). Published in 1994. Pages 134 - 135.
- "The Scottish Clans and Their Tartans”. W. & A. K. Johnston Limited. Edinburgh and London. 1886. Page 20.
- Way, George and Squire, Romily. Collins Scottish Clan & Family Encyclopedia. (Foreword by The Rt Hon. The Earl of Elgin KT, Convenor, The Standing Council of Scottish Chiefs). Published in 1994. Pages 84 - 85.
- Way, George and Squire, Romily. Collins Scottish Clan & Family Encyclopedia. (Foreword by The Rt Hon. The Earl of Elgin KT, Convenor, The Standing Council of Scottish Chiefs). Published in 1994. Pages 258 - 259.
- "FARQUHARSON OF INVERCAULD, CHIEF OF FARQUHARSON".
- "Faquharson Clan UK".