The FA alleges that the Premiership champions breached Rule E25 by testing on 12 July 2004.
The rule says: "The independent private testing/screening of players by clubs, club officials or any other person subject to FA rules is prohibited."
Chelsea have been given until 23 September to respond to the charge.
The FA does not allow independent testing in case it leads to incidents where clubs could try to cover up drug use by squad members.
There is no suggestion that Chelsea, who have twice had high-profile players test positive for cocaine within the past three years, have attempted any sort of cover-up.
Chelsea have taken a strong line against drugs in the past, sacking striker Adrian Mutu in October last year for taking cocaine.
They took the same action against Australian keeper Mark Bosnich in January 2003 after he also tested positive for cocaine.