A video shared on social media showed the helicopter landing at the club's Mash Barn Lane training complex at around 1.20pm.
A spokesman for the club said the emergency services were responding to a medical incident at a junior game, where an opposition player was injured.
The player is expected to make a full recovery, the spokesman said.
The American Express Elite Football Performance Centre opened in 2014, three years after Brighton and Hove Albion's Amex Stadium was opened.