The Commissioner's Cup is awarded to the member institution with the best overall record in conference competition in a single academic year. Points are awarded based on each school's finish in conference sports that include a conference championship.
| 2010-11 |
Dickinson State (79 pts) |
Black Hills State (75 pts) |
Jamestown College (68.5 pts) |
Minot State (62 pts) |
South Dakota Mines (41 pts) |
Valley City State (33 pts) |
Dakota State (29.5 pts) |
Mayville State (15 pts) |
| 2009-10 |
Dickinson State (115 pts) |
Black Hills State/Jamestown (110 pts) |
Minot State (88 pts) |
South Dakota Mines (61 pts) |
Dakota State (57.5 pts) |
Valley City State (51 pts) |
Mayville State (24.5 pts) |
|
| 2008-09 |
Dickinson State (120 pts) |
Black Hills State (113 pts) |
Jamestown (101 pts) |
Minot State (96 pts) |
South Dakota Mines (62 pts) |
Dakota State (60 pts) |
Valley City State (34 pts) |
Mayville State (27 pts) |
| 2007-08 |
Jamestown / Black Hills St. |
Dickinson St. |
Minot St. |
Dakota St. |
South Dakota Mines |
Mayville St. |
Valley City St. |
|
| 2006-07 |
Dickinson St. (110 pts) |
Jamestown (105.5 pts) |
Black Hills St. (95 pts) |
Minot St. (73 pts) |
South Dakota Mines (68.5 pts) |
Dakota St. (64 pts) |
Valley City St. (51 pts) |
Mayville State (40 pts) |
| 2005-06 |
Dickinson St. (116 pts) |
Jamestown (98.5 pts) |
Minot St. (97.5 pts) |
Black Hills St. (91 pts) |
Dakota St. (69 pts) |
South Dakota Tech (49 pts) |
Valley City St. (45 pts) |
Mayville State (36 pts) |
| 2004-05 |
Univ. of Mary (166.5 pts) |
Jamestown (139 pts) |
Dickinson St. (129.5 pts) |
Minot St. (120 pts) |
Dakota St. (96.5 pts) |
Black Hills St. (76 pts) |
South Dakota Tech (74 pts) |
Si Tanka-Huron (43 pts) |
Mayville St. (41.5 pts) |
Valley City St. (39 pts) |
| 2003-04 |
Dickinson St. (146 pts) |
Univ. of Mary (139 pts) |
Jamestown (136 pts) |
Minot St. (121 pts) |
Black Hills St. (106 pts) |
Dakota St. (83 pts) |
South Dakota Tech (69 pts) |
Si Tanka-Huron (55 pts) |
Valley City St. (35 pts) |
Mayville St. (30 pts) |
| 2002-03 |
Univ. of Mary (140 pts) |
Dickinson St. (131 pts) |
Jamestown (127.5 pts) |
Minot St. (116.5 pts) |
Black Hills St. (90 pts) |
Dakota St. (87 pts) |
South Dakota Tech (81 pts) |
Valley City St. (61 pts) |
Si Tanka-Huron (53 pts) |
Mayville St. (40 pts) |
| 2001-02 |
Univ. of Mary (135 pts) |
Jamestown (125.5 pts) |
Dickinson St. (116 pts) |
Minot St. (105 pts) |
Black Hills St. (103 pts) |
South Dakota Tech (82.5 pts) |
Dakota St. (70 pts) |
Valley City St. (60 pts) |
Mayville St. (52 pts) |
Huron Univ. (40 pts) |
| 2000-01 |
Jamestown (108 pts) |
Univ. of Mary (107 pts) |
Minot St. (101 pts) |
Dickinson St. (97.5 pts) |
Black Hills St. (93 pts) |
Valley City St. (76.5 pts) |
Dakota St. (75 pts) |
Huron Univ. (72.5 pts) |
Mayville St. (66 pts) |
South Dakota Tech (60.5 pts) |