The 51-year-old mother of three disappeared on February 4 and despite several police searches, her body has not been found.
Patrick Orren Stephenson faced Ballarat Magistrates Court on Thursday via video link from prison, wearing a white T-shirt with a beard, long hair and a black watch.
The 23-year-old has been charged with Ms Murphy's murder at Mount Clear, near Ballarat, after she disappeared.
Patrick Orren Stephenson has pleaded not guilty to the murder of missing woman Samantha Murphy. (Joel Carrett/AAP PHOTOS)
Ms Murphy's husband Mick attended the brief hearing, marking the first time he has presented at court in person since his wife's alleged killing.
Prosecutor Raymond Gibson KC informed the court that Stephenson had elected to stand trial in the Supreme Court over the murder.
This will mean Stephenson does not face a committal hearing to test the evidence in the lower court.
Defence barrister Michael Allen said his client understood his rights in electing to fast track the case.
Magistrate Mark Stratmann committed Stephenson to stand trial and asked him to enter a plea of guilty or not guilty to the murder charge.
"Not guilty Your Honour," Stephenson responded.
He will be remanded in custody to next face the Supreme Court for a directions hearing on November 27.
Stephenson is the son of former AFL player Orren Stephenson, who played 15 games for Geelong and Richmond between 2012 and 2014.
Several search efforts mounted by police have failed to find missing mother Samantha Murphy. (David Crosling/AAP PHOTOS)
Ms Murphy was last seen leaving her home on Eureka Street, Ballarat, to go for a run on the morning of February 4.
Since then, police have launched multiple searches searches in different areas of bushland to find Ms Murphy's body, including Enfield State Forest in September.
Stephenson is separately facing driving offences over a collision with a motorcycle months before Ms Murphy's disappearance.
He has been charged with careless driving, drink driving and drug driving after a crash on October 1 in 2023, the Sunday after the AFL grand final.