The 2003 CIS football season began on August 29, 2003, and concluded with the 39th Vanier Cup national championship on November 22 at the SkyDome in Toronto, Ontario, with the Laval Rouge et Or winning their second championship. Twenty-seven universities across Canada competed in CIS football this season, the highest level of amateur play in Canadian football, under the auspices of Canadian Interuniversity Sport (CIS).

Note: GP = Games Played, W = Wins, L = Losses, OTL = Overtime Losses, PF = Points For, PA = Points Against, Pts = Points

Teams in bold have earned playoff berths.

Ranks in italics are teams not ranked in the top 10 poll but received votes.
NR = Not Ranked.

The Vanier Cup was played between the champions of the Mitchell Bowl and the Uteck Bowl, the national semi-final games. In 2003, the Uteck Bowl replaced the long-standing Churchill Bowl, which had been competed for since 1989 as a national semi-final game. Along with the Mitchell Bowl, the semi-final games now worked on a fully rotating basis, with the winners of the Canada West conference Hardy Trophy visiting the winners of the Atlantic conference Loney Bowl championship for the Uteck Bowl. The Ontario conference's Yates Cup championship team hosted the Dunsmore Cup Quebec champion for the Uteck Bowl.

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