His lawyer told the court Mr Houston would be pleading not guilty to the crime of concealing a serious indictable offence of another person.
The case will next be before the court on 23 November.
Mr Houston stands accused of concealing a serious indictable offence allegedly committed by his father.
Police will say that Frank Houston indecently assaulted a male in 1970.
Court documents allege that between 1999 and his father's death in 2004, Brian Houston believed his father had committed the crime.
Police will argue that he knew information that could help secure the prosecution of his father and failed to bring it to the attention of police.
Mr Houston had promised when charged in August to "set the record straight".
"These charges have come as a shock to me given how transparent I've always been about this matter," he said at the time.
NSW Police investigated the matter for two years after the allegation was raised in media and the institutional child abuse royal commission.
Since being charged, Mr Houston has stepped down from the board of Hillsong, the church he founded with wife Bobbie in Sydney's Hills district in 1983.
Now a global empire, the church says 150,000 people in 30 countries attend its services and 50 million people sing its songs each week.
Anyone seeking information or support relating to sexual abuse can contact Bravehearts on 1800 272 831 or Blue Knot on 1300 657 380.