| Year: | 1946 |
| Team: | Houston Cougars |
| Sport: | football |
| Conference: | Lone Star Conference |
| Short Conf: | LSC |
| Record: | 4–6 |
| Conf Record: | 1–4 |
| Hc Year: | 1st |
| Stadium: | Public School Stadium |
| Prev Year: | none |
The 1946 Houston Cougars football team represented the University of Houston in the 1946 college football season as a member of the Lone Star Conference (LSC). The Cougars were led by head coach Jewell Wallace in his first season and finished with a record of four wins and six losses (4–6 overall, 1–4 in the LSC).