Christopher Stevenson, 25, is accused of making the comment saying "think I might assassinate Alex Salmond" on January 28.
He is alleged to have behaved in a "threatening or abusive manner which was likely to cause a reasonable person to suffer fear or alarm".
Mr Stevenson, from Glasgow's East End, was arrested and taken to London Road police office before appearing at Glasgow Sheriff Court from custody and entering a not guilty plea.
A trial - which will take place before a sheriff only - was set for August. Stevenson was released from custody and ordained to appear on the next occasion by Sheriff Norman Ritchie QC.
On Mr Stevenson's Twitter page @ChrisTastic he appears to have since posted a number of tweets about the alleged comment.
These include "Feel I've upset the Yes campaigners, they want me to go to jail for that tweet last night" and "Ridiculous that even a joke makes you a criminal".
The Twitter page is now private and tweets are no longer public.
His trial is set to take place two months after Dogan Arslan, 47, is to go on trial for allegedly staring at Nicola Sturgeon at her Pollokshaws Road office.
Mr Arslan, from Battlefield, in Glasgow's south side, is alleged to have carried out the offence between October and December 2012, from his car.
It is claimed he "engaged in course of conduct" which caused people in the office, including the Deputy First Minister, "fear and alarm" and that he "repeatedly loitered within a parked motor vehicle in the vicinity of the office premises" and stared at the offices and Ms Sturgeon.