Farquhar McGillivray Knowles was born in Elora Village, Nichols Twp., Wellington Co., Ontario, Canada on May 22, 1859. His parents were Scottish in origin. In 1863 Knowles was educated in Guelph, Ontario. Due to the influence of his grandfather Thomas Knowles (Royal Hibernian Marine) Farquhar enrolled in the artillery at the military academy in West Point around 1877. He suffered a serious accident in his fourth year which ruled out a military career.
Knowles found work in New York City retouching photographs, and took some art courses there. He returned to Canada where he found employment with the William Notman and John Fraser photographic studios in Toronto. He added color to their portrait photographs of wealthy customers. The studio's co-owner was John Arthur Fraser, R.C.A., an accomplished watercolor artist, who instructed him in painting miniatures and watercolors. In 1885 McGillivray Knowles went to Europe, where he studied painting in England and France. Knowles married Ada Cullen, who died in 1887.