The Chief Magistrate, Mrs A. Ipaye-Nwachukwu, said the accused should approach the sexual offences court to secure his bail and adjourned the matter until June 27 for mention.
The police had arraigned Nnanna on a two counts for unlawful sexual intercourse and threat to life.
He, however, pleaded not guilty to the charges.
The prosecutor, Chinalu Uwadione, had told the court that the accused committed the offences at Ilaje Village, Ebute Meta West, on May 4 about 10 p.m.
Uwadione said the accused had threatened to stab the 13-year-old with a knife if she refused to allow him have his way.
The offence violates sections 56 and 137 of the Criminal Law of Lagos State, 2015, the prosecutor said.