Douglas Fleming, 49, has been charged with killing Martin Toner, whose body was found in a field near Langbank, Renfrewshire, in July 2004.
Mr Fleming, from the Aviemore area, also faces one count of attempting to pervert the course of justice.
He made no plea or declaration before Paisley Sheriff Court and has been bailed pending further examination. He is due to appear in court again at a later date.
Ever since the discovery of Mr Toner's body on July 13, 2004, detectives have been working to piece together the events leading up to his disappearance.
Police were initially concerned for the father-of-two after he was reported missing by his wife two weeks previously, on June 29. Earlier that day, Mr Toner had visited a gym near to his home in Pollokshields, Glasgow, but had travelled to Langbank shortly after.
He was last seen in the town's Main Street at around 3pm, after being dropped off at the train station nearby.
His mobile phone and training bag have never been recovered and it still remains unclear why he had been in the Langbank area that day.
According to investigators, Mr Toner met a "very violent death" and they confirmed he had not been killed at the site where his body was found.
It was also revealed he could have been dead for up to eight days beforehand.
At the time of his death, Mr Toner was under investigation for alleged drug trafficking offences and was due to appear in court on July 14 - the day after his body was found. Police have suggested these criminal allegations may have hindered their inquiries, with witnesses failing to come forward in fear of any repercussions.
A reward of £3000 was also issued for any information which led to a conviction.
In 2011, a 46-year-old man was reported to the procurator fiscal in connection with Mr Toner's death.