The Philippines participated at the 20th Southeast Asian Games held in Brunei from 7 to 15 August 1999.

The Philippines fell to fifth place in the overall medal tally, their lowest finish since joining the SEA Games in 1977.

World pool champion Efren 'Bata' Reyes and golfer Gerald Rosales were the only Filipino double gold medalists in the 1999 edition of the Games.

The Nationals captured their fifth straight basketball gold, defeating main rival Thailand, 89–69.

Philippine Olympic Committee president Celso Dayrit announced a four-year intensive elite sports development plan which the POC will undertake.