James Aitken Wylie (9 August 1808 – 1 May 1890) was a Scottish historian of religion and Presbyterian minister.

His name-father, Rev James Aitken, was an Auld Licht Anti-burgher minister in the Secession Church.

He published his book The Papacy: its History, Dogmas, Genius, and Prospects in 1851, winning a prize of a hundred guineas from the Evangelical Alliance.

Wylie's classic work, The History of Protestantism (1878), went out of print in the 1920s, although it was briefly reprinted in Northern Ireland in a two-volume reproduction in the late 20th century.

He is buried with his wife, Euphemia Gray (1808–1845) and their children, in East Preston Street Burial Ground.