The stepfather of a little girl who died from serious injuries on the New South Wales mid-north coast has been charged with her rape and murder.

The two-year-old girl was taken to Coffs Harbour hospital on April 20, but she lost consciousness while being treated.

She died the next morning from her injuries.

The child abuse squad and homicide detectives investigated the death.

Coffs Harbour crime manager Darren Jameson says the 23-year-old man was arrested on Thursday afternoon.

"He is related to the child, in fact he is the child's stepfather," he said.

"He's been charged with murder and aggravated sexual assault of a child under 10.

"We will allege in court that he sexually assaulted the child and delivered a number of serious blows to her abdomen which caused an injury which later led to her death.

"There are drug charges - he's been charged with possession of drugs. We'll allege that they are methylamphetamine."

The man faced court today but did not enter a plea or apply for bail.

The case was adjourned until July 22.