The girl, who has Smith-Magenis Syndrome, was arrested four times and twice held overnight in police stations.
Her mother complained about her treatment to the Independent Police Complaints Commission (IPCC).
Sussex Police said it welcomed the IPCC scrutiny and supported its inquiry.
The girl came into contact with police between 2 February and 2 March last year in Horsham, West Sussex.
She was held under under the mental health act on 9 February, arrested on suspicion of assault seven days later, held over a public order offence on 29 February and arrested in connection with criminal damage on 2 March.
The girl's mother complained in July 2012 about the methods of restraint used on her daughter, which the IPCC said appeared to have included handcuffs and leg restraints, and the decisions to hold her in police cells overnight.
Commissioner Mike Franklin said: "The IPCC investigation is examining the nature and circumstances of the officers' interaction with the girl to determine whether the degree of force and method of restraint used by officers was appropriate and in accordance with the law, the officers' training and force policy and procedure.
"The investigation is also looking at the appropriateness of the decision to place the girl in police cells on four occasions and to refer her to the Crown Prosecution Service for charging on one occasion.
"These are very serious complaints about the treatment of an 11-year-old girl suffering from Smith-Magenis Syndrome and I will ensure that they are investigated thoroughly."
The Smith-Magenis Syndrome Foundation UK said major features of the condition include mild to moderate intellectual disability, delayed speech and language skills, distinctive facial features, sleep disturbances, and behavioural problems.
Sussex Police is being investigated over the treatment of a disabled 11-year-old girl who was physically restrained on five occasions.