Prosecutors says 36-year-old Mohammad Khan, of Cambridge, used excessive force to detain the girl at Primark on June 9.
He allegedly pulled the girl back into the store, threw her to the ground, straddled her and punched her in the face.
Khan and his employer, Securitas Services USA Inc., were charged Wednesday with assault and battery on a child under 14.
Authorities say Khan has been reprimanded on at least four previous occasions for using more force than allowed.
Police say the girl tried to steal about $175 worth of clothing. She is too young to be charged.
No attorney was listed for Khan in court records. A message was left with Securitas.
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