1999 Cal Poly Mustangs football team

The 1999 Cal Poly Mustangs football team represented California Polytechnic State University during the 1999 NCAA Division I-AA football season.

Cal Poly competed as an NCAA Division I-AA independent in 1999. The Mustangs were led by third-year head coach Larry Welsh and played home games at Mustang Stadium in San Luis Obispo, California. The Mustangs finished the season with a record of three wins and eight losses (3–8) for the second consecutive year. Overall, the team was outscored by its opponents 246–345 for the season.