The 1946 Cal Poly Mustangs football team represented California Polytechnic School—now known as California Polytechnic State University, San Luis Obispo—as am independent during the 1946 college football season.
Led by Howie O'Daniels, who returned for his tenth season as head coach after having helmed the team from 1933 to 1941, the Mustangs compiled a record of 6–2–1.
The team outscored opponents 152 to 88 for the season.
Cal Poly played home games at Mustang Stadium in San Luis Obispo, California.
The Mustangs played two games against non-collegiate military teams, San Diego Naval Training Station and the El Toro Marines.