The Belgian's attempt to kick the ball out from under the time-wasting youngster is alleged to be violent conduct, and the FA deemed a red card insufficient punishment.
Charlie Morgan, 17, attempted to prevent the Belgian from taking back the ball as the Blues desperately pushed for a comeback in Wednesday's second leg of the Capital One Cup semifinal. The 22-year-old was then red-carded for violent conduct after he kicked at the ball, which the ball boy had trapped under his body.
A statement on the FA's official website explained: "It is alleged that Hazard's behavior ... constituted violent conduct whereby the standard punishment that would otherwise apply was clearly insufficient."
The former Lille star has until Tuesday to respond to the charge.
While charging Hazard, the FA statement indicated that the ball boy's behavior would also need to be addressed.
"The FA will remind all clubs of their responsibilities in ensuring ball boys and other personnel around the pitch act in an appropriate manner at all times and will liaise with competitions accordingly," the FA wrote.