The SUNY Cortland intercollegiate athletics program finished first in the State University of New York Athletic Conference (SUNYAC) Commissioner's Cup standings for the 2009-10 school year. Cortland has won the Commissioner's Cup, which is awarded for overall sports excellence, in 13 of the 14 years that it has been awarded, including the last seven seasons. Cortland finished with an average score of 8.46 points. Geneseo was second with an average score of 8.26 points.

Commissioner's Cup points are awarded based on each team's finish in the SUNYAC standings, both during the regular season and in league postseason tournaments, when applicable. The first-place school in each sport receives 10 points, second place receives nine points, and so on. A school's regular-season finish is added to its postseason finish and is divided by two to determine the points for each sport. The total points earned are then divided by the number of conference sports the school sponsors.

Cortland won five league crowns – field hockey in the fall, women's basketball in the winter, and men's lacrosse, women's lacrosse and softball in the spring. The Red Dragons were also league runner-up in 10 sports – men's cross country, women's cross country, women's soccer, women's volleyball, men's indoor track and field, men's swimming and diving, women's swimming and diving, men's outdoor track and field, women's outdoor track and field, and baseball (tied for second). The SUNYAC sponsors 20 sports.

2009-10 SUNYAC Commissioner's Cup — Final Standings

Rank, School	# of league sports	Total Points	Avg. Points per sport
1. Cortland	20	169.25	8.46
2. Geneseo	19	157.00	8.26
3. Oneonta	19	133.25	7.01
4. Brockport	20	122.75	6.14
5. Plattsburgh	16	95.00	5.94
6. New Paltz	14	79.00	5.64
7. Fredonia	18	96.75	5.38
8. Buffalo St.	16	81.00	5.06
9. Oswego	20	83.50	4.18
10. Potsdam	* 12	37.75	3.15

 

* Potsdam sponsors 13 SUNYAC sports, but its women's cross country team did not have enough runners compete at the SUNYAC Championships to register a team score.