Murdoch MacKinnon (March 15, 1865 – October 12, 1944) was a Canadian politician and served as the 11th Lieutenant Governor of Prince Edward Island.

He received his higher education from Prince of Wales College and then became a farmer.

From that point until the 1919 General Elections, MacKinnon was continuously re-elected and retained his seat in the Legislature.

On September 8, 1919, Murdoch MacKinnon was appointed Lieutenant Governor of Prince Edward Island and served in that capacity until 1924.

He is best known for making constitutional history in the province in 1923 for refusing his assent to the Church Union Bill.