| Santosh Trophy | |
| Year: | 1989–90 |
| Other Titles: | National Football Championship |
| Winners: | Goa |
| Count: | 3 |
| Second: | Kerala |
| Prev Season: | 1988–89 |
| Next Season: | 1990–91 |
The 1989–90 Santosh Trophy was the 46th edition of the Santosh Trophy, the main State competition for football in India. It was held in Margao, Goa. Goa defeated Kerala 2–0 in the final to win the competition for the third time. Kerala finished second for the third straight year.
From this season, the tournament was limited to players who were under 23 years.