The 2003 Cal Poly Mustangs football team represented California Polytechnic State University during the 2003 NCAA Division I-AA football season. 2003 was the last year Cal Poly competed as an NCAA Division I-AA independent. In 2004 they would become a charter member of the new Great West Football Conference. The 2003 Mustangs were led by third-year head coach Rich Ellerson and played home games at Mustang Stadium in San Luis Obispo, California. The team finished the season with a record of three wins and eight losses (7–4). Overall, the team outscored its opponents 316–241 for the season.