Judge Brooke Gibson remanded Fawcett in custody by consent to reappear in Christchurch District Court.
He said that was the court room closest to the place where the crimes were alleged to have been committed.
Fawcett will reappear on Monday when he is expected to apply for bail.
According to the charge sheets, the murder and kidnapping happened on December 18 in 2008.
Earlier today Ms Manning's brother, Robin Manning, said he had been told by police an arrest had been made or was imminent.
"It's great news,'' he said.
"It definitely wasn't expecting it. I thought it might take a bit longer. It's been well over three years (of waiting).''
Ms Manning's extensively injured body was found dumped in the Avon River on December 19, 2008.
Investigators believe she was attacked at a large section on Galbraith Avenue, which was being used by the Mongrel Mob at the time of her murder.
Last September, it was revealed Ms Manning, 27, was also sexually assaulted, and a semen sample had been recovered from her body.
The semen would have been left at the time of her death or very close to it and could provide a DNA profile of someone who had sex with Ms Manning, a local prostitute, around the time of the murder, police said.
Police earlier ruled out that the arrested man was linked to the unidentified semen sample but that he was identified as a person of interest early in the investigation.
Investigation head Detective Inspector Greg Williams said at the time of the murder the accused man was living in Christchurch and he has "definite links'' to the property where Ms Manning is alleged to have been killed.
"From evidence gathered it is clear that a number of people have been involved in either the kidnapping or murder of Ms Manning.
"The inquiry is continuing to identify all persons who were responsible for her death, or were accessories after the fact, so that they can be bought to justice.''
Police expect to interview a number of people associated with the accused man over the next few days.
The man arrested today has been ruled out as being linked to an unidentified semen sample found on Ms Manning's body.
Police said the man arrested was identified as a person of interest early in the investigation.
Mr Williams would not comment of whether the arrested man had gang affiliations.
