McGinnis grew up in Manhattan, New York. He attended the Collegiate School in the Upper West Side, and as a senior in 1996–97, averaged 23 points, 15 rebounds and six blocks per game. He chose Dartmouth over other Ivy League schools Penn, Princeton and Harvard largely in part because his father is an alumnus and his brother was a student there at the time. He also cited the potential of getting a lot of playing time as a freshman as another reason for choosing the Big Green. A 6 ft 8 in (2.03 m) center, McGinnis finished his career at Dartmouth with close to 900 points and over 1,000 rebounds.