In his four years as commissioner, Larry Scott has transformed the stately, sleepy Pacific-10 Conference into the big-business Pac-12, expanding the conference and quadrupling its annual television-rights revenue. Scott cashed in on his aggressive moves in 2011-12, earning more than $3 million, according to tax documents released by the conference Sunday. That appears to be the highest compensation ever for a sitting college commissioner.

Scott took home a $1,376,000 bonus in addition to a base salary of $1,575,000 and other...