The 1999–2000 Santosh Trophy qualifiers began on 19 March and ended on 8 April 2000.
Six teams — Sikkim, Mizoram, Andaman and Nicobar, Nagaland, Arunachal Pradesh and Meghalaya — pulled before the start of the competition reducing the number to 22.
Following the round-robin stages, eight teams played the play-offs, and Services, Punjab, Karnataka and Maharashtra made it to the final round.
Assam were up 1–0 after a 20th minute penalty kick conversion by Akom Ao.
[2] The winner of each 'cluster' played a play-off game each and the final two qualification spots were determined.