Has a College Football game ever ended 39-6?
It has. 39-6 has been a College Football final 52 times in 84,433 games. The first was Princeton beat Pennsylvania on November 3, 1883; the latest was Vanderbilt beat Chattanooga on September 12, 1970.
That makes 39-6 the 375th most common final score out of 2,216 that have ever occurred in College Football. One point away, 40-6 has happened 98 times and 39-7 has happened 68 times.