The school opened in 2004 as a result of new residential development in the eastern Auckland area.

[1] Botany Downs Secondary College was announced with a notice published in the New Zealand Gazette by Education Minister Trevor Mallard on 12 November 2001, with the working name Howick South Secondary School.

[3] The school opened in January 2004, initially taking Year 9 students only.

The logo design uses the circles of the Beta and Delta characters from the Greek alphabet.

Other major ethnic groups include Pacific (8.2%), Māori (5.5%), Middle Eastern, Latin American, African (MELAA) (4.8%), and other (0.8%).