A 19-year-old man accused of having sex with a 13-year-old girl was "obsessed" with her and threatened to kill himself if he was sent to jail, a court has heard.

The ACT Magistrates Court was told the girl had fallen pregnant and had an abortion during the relationship, which had spanned at least 18 months and police were considering further charges against the man.

The man's name, and the names of several witnesses in the case, have been suppressed to protect the alleged victim's identity.

He was charged with one count of sexual intercourse with a child aged under 16.

Police allege the man committed the offence between February and March last year (2011).

The court heard the girl, who was in the care of authorities, had been the subject of a care and protection order banning the young man from contacting her but the pair were caught by police at his brother's home in Belconnen.

His defence lawyer told the court her client suffered from symptoms of depression and had attempted suicide three weeks ago, after he was labelled a pedophile.

The court heard he was immature for his age, was scared for his welfare in jail and had threatened to kill himself if remanded in custody.

It was argued that police could seek a domestic violence order against the young man which would also prevent him from contacting the girl, but had so far failed to do so. 

But the prosecution argued the man had known the relationship was inappropriate for some time but had still persisted with it.

The prosecution also argued the man could be placed in protective custody at the Alexander Maconochie Centre which would help deal with the risk of suicide or self harm.

Magistrate Bernadette Boss said she was concerned by the degree of "obsession" on the part of the young man and the girl.

She noted that the man could be placed in protective custody, but balanced that against his youth and the fact that he could be in custody for a lengthy period.

Dr Boss granted bail on strict conditions, including a night time curfew and a ban on contacting or going within 100m of the girl.