John Fraser was born on March 22, 1827 in Cromarty, Scotland. He graduated from the University of Aberdeen in 1844. Shortly after graduation, he sailed to Bermuda to take charge of an academy on the island. Records do not detail how long he spent in Bermuda, but by 1855 he was in the United States and a professor of mathematics and astronomy at Jefferson College in Pennsylvania.

Fraser left Jefferson in 1862 in order to serve in the Union army. A well-loved and charismatic professor, in 10 days he managed to persuade 100 young men to join him. From 1862 until the close of the war, Fraser served in the 140th Pennsylvania Volunteer infantry. In 1864 he was captured by Confederate forces and imprisoned. While imprisoned, sources say he could be observed lecturing his comrades on Shakespeare and mathematics amid the squalid confines of their living conditions. In November 1864, he authored a petition demanding better living conditions for his fellow prisoners of war. In 1865 he was exchanged, and he served until the end of the war.

Fraser was the President of the Agricultural College of Pennsylvania when he was selected by Chancellor Oliver as a successor. He was elected to office on December 4, 1867 and he served concurrently as Chancellor and as Professor of Mental and Moral Philosophy and Belles-Lettres. During his tenure, KU expanded in size, both in terms of the number of students as well as the number of buildings.

One of Fraser's greatest and most remembered contributions to the University was erecting the second building on campus, University Hall, later known as Fraser Hall. In 1869, he convinced the community and the Board of Regents to raise a $10,000 bond, which matured to $90,000. Fraser persuaded the State Legislature to add $50,000 to the funding, and University Hall was built. When the hall was completed, it was lauded as one of the most modern university buildings in the country. Time signals in classrooms were controlled by a single clock powered by electricity, gas jets in the lecture hall could be ignited by electricity, it was heated and ventilated with steam, plumbing and wires were concealed in the walls, and the lecture halls were constructed using the principle of panoptic curves, so that each row sat slightly higher than the one in front of it. Fraser's building was a KU landmark until 1965, when it was razed and the current Fraser Hall was erected in its place.

Amid faculty discontent, Fraser left the University of Kansas in fall 1874 when the state legislature cut funding for the university by 33 percent.

Fraser served as the Kansas State Superintendent of Public Instruction from 1875 to 1876. He then returned to Pennsylvania and served as Professor of Political Economy and International Law at the Western University of Pennsylvania until his death of varioloid, a form of smallpox, on June 4th, 1878.