Sion Jenkins, 39, a deputy head teacher, has also been charged with dishonestly obtaining his job by lying about his qualifications and his teaching experience.
Billie-Jo was beaten over the head with a metal tent peg and was reported to have been found by one of her four stepsisters and Mr Jenkins at their home in Hastings, East Sussex, on 15 February.
The schoolgirl had been painting the patio doors.
Mr Jenkins was remanded in custody for a week at a special sitting of Hastings Magistrates court yesterday afternoon, 24 hours after being arrested for the second time.
The father of four spoke only to give his name and address during the 30-minute hearing. Smartly dressed in a blazer, blue-and-white checked shirt and fawn trousers, he remained impassive throughout the proceedings, occasionally bowing his head as two charges were read out in court.
Along with being charged with the murder of his foster daughter, he also faces a charge that between 10 December 1991 and 14 March 1997 he dishonestly obtained for himself employment by deception, namely by falsely representing his academic qualifications and teaching experience.
An application for bail was refused. Soon after the hearing Mr Jenkins was taken to Lewes prison.
He was due to take over as headmaster of the William Parker School, in Hastings, in September, and has been on compassionate leave since the murder.
Mr Jenkins and his wife Lois, 35, a social worker, have been living apart since his initial arrest on 24 February.
After the murder, Mr Jenkins and his wife made a public appeal for help to track down the killer. He told reporters that he had seen a stalker in the back garden and that Billie-Jo and his family had been worried about their safety.
He was arrested for the first time on 24 February and questioned for a day-and-a-half before being released on bail.
Mrs Jenkins returned to live at the house a few days ago after staying with relatives and this morning took her four children to school. Mr and Mrs Jenkins had fostered Billie-Jo for five years and last December became her legal guardians.
Mr Jenkins' solicitor, Brendan Salsbury, said his client "categorically denied" the murder charge.